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NCBI C++ ToolKit: src/objmgr/util/sequence.cpp Source File

((**it).IsSource())

&(**it).GetSource();

cleaned_location->

(*cds_loc);

cleaned_location->

(*rev_loc);

scope.GetTaxId(idh);

& bioSource = pSourceFeat->GetData().GetBiosrc();

(!bioSource.CanGetOrg()) {

bioSource.GetOrg().GetTaxId();

& bioSource = pSourceFeat->GetData().GetBiosrc();

(bioSource.CanGetOrg()) {

pOrgRef = &bioSource.GetOrg();

(!pSource || !pSource->CanGetOrg()) {

&pSource->GetOrg();

&pSourceFeat->GetData().GetBiosrc();

vector<CSeqdesc::E_Choice>

;

( desc.

() ) {

((**it).IsMolinfo())

&(**it).GetMolinfo();

( ; desc_iter; ++desc_iter) {

}

(exception&) {

);

vector<CMappedFeat> best_feats;

( range.

() > seq_length ) {

( length > best_length ) {

best_length = length;

( length == best_length ) {

best_feats.push_back(*it);

( best_feats.empty() ) {

);

( best_feats.size() > 1 ) {

);

best_feats[0].GetData().GetProt().GetLabel(&ret);

);

(GetErrCode()) {

(

*

(

.GetPointer()));

(

*

(

.GetPointer()));

(

*

(

.GetPointer()));

(

*

(

.GetPointer()));

(

*

(

.GetPointer()));

);

);

(!idh)

ret;

idh.

())

idh;

(db ==

|| db ==

)

idh;

(exception& e) {

(

<<e.what());

);

);

( idh.

() ) {

idh.

();

(exception& e) {

);

( idh.

() ) {

idh.

();

);

);

);

( rec.

().empty() ) {

* scope,

* frame)

(base_frame > 0) {

*frame = (3 + rl.

.front()->GetFrom() - base_frame) % 3 + 1;

<<

);

(*it)->SetFrom(((*it)->GetFrom() - base_frame) / 3);

(*it)->SetTo (((*it)->GetTo() - base_frame) / 3);

rl.

(scope, rl_flags);

(base_frame > 0) {

nuc_length, prot_length;

from = (*it)->GetFrom() * 3 + base_frame;

to = (*it)->GetTo() * 3 + base_frame + 2;

(*it)->SetFrom(from);

<

T,

U>

(

pair<T,U>& p1,

pair<T,U>& p2)

p1.first < p2.first;

<

T,

U>

(

pair<T,U>& p1,

pair<T,U>& p2)

p1.second < p2.second;

( gene1.first != gene2.first ) {

gene1.first < gene2.first;

&loc1 = gene1.second->GetLocation();

&loc2 = gene2.second->GetLocation();

( gene1.second->IsSetData() && gene1.second->GetData().IsGene() &&

gene2.second->IsSetData() && gene2.second->GetData().IsGene() )

gene1.second->GetData().GetGene().

( &gene1_label );

gene2.second->GetData().GetGene().GetLabel( &gene2_label );

gene1_label < gene2_label;

revert_locations =

;

(overlap_type) {

revert_locations =

;

( bioseq_handle ) {

circular_id = bioseq_handle.

();

* loc_id =

;

(exception&) {

circular_id.

(loc_id);

(

<< e.what()) ;

(circular_id && range.

() > range.

()) {

sub_loc->

().Assign(*circular_id);

sub_loc->

().Assign(*circular_id);

( ! circular_id && range.

() > range.

() ) {

unique_ptr<CFeat_CI> feat_it_ptr;

circular_length, range, loc, sel, scope, strand);

( circular_loc ) {

( !bioseq_handle ) {

feat_it_ptr.reset(

(scope, *circular_loc, sel) );

( bioseq_handle ) {

feat_it_ptr.reset(

(bioseq_handle, range, strand, sel) );

feat_it_ptr.reset(

(scope, loc, sel) );

cleaned_loc->

( loc );

plugin->

( bioseq_handle, cleaned_loc, circular_length );

( ; feat_it; ++feat_it) {

overlap_type_this_iteration = overlap_type;

revert_locations_this_iteration = revert_locations;

shouldContinueToNextIteration =

;

shouldContinueToNextIteration,

cleaned_loc_this_iteration,

overlap_type_this_iteration,

revert_locations_this_iteration,

annot_overlap_type);

( shouldContinueToNextIteration ) {

( !revert_locations_this_iteration ) {

*cleaned_loc_this_iteration,

overlap_type_this_iteration,

*cleaned_loc_this_iteration,

overlap_type_this_iteration,

*candidate_feat_loc,

overlap_type_this_iteration,

*candidate_feat_loc,

overlap_type_this_iteration,

candidate_feat_loc, scope, sel, circular_length );

feats.push_back(sc);

(exception&) {

(

);

std::stable_sort(feats.begin(), feats.end(),

overlap_type, scores, scope, opts, plugin );

(scores.size()) {

scores.back().second;

scores.front().second;

overlap_type, scores, scope, opts, plugin );

(scores.size()) {

scores.back().second;

scores.front().second;

has_xref =

;

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

search_both_strands =

)

(scores.size()) {

overlap = scores.front().second;

(search_both_strands && !overlap) {

(scores.size()) {

overlap = scores.front().second;

search_both_strands)

scope, search_both_strands);

search_both_strands)

search_both_strands);

( eTransSplicing ) {

( !it ) ret.

();

( it ) ret.

();

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

((*it)->GetQual(),

)) {

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

(*it)->GetData().GetGene().IsSetPseudo() &&

(*it)->GetData().GetGene().GetPseudo()) {

(gene &&

(*gene, scope)) {

p->GetSeq_feat();

p->GetSeq_feat();

((*xit)->IsSetData() && (*xit)->GetData().IsGene() && (*xit)->GetData().GetGene().IsSuppressed()) {

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

(!(*xit)->IsSetData() || (*xit)->GetData().IsGene())) {

(far_feats.size() > 0) {

far_feats.front().GetSeq_feat();

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

}

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

& gene = (*xit)->GetData().GetGene();

feats, scope, opts, plugin );

(feats.size() < 2) {

(feats.size() == 1) {

mrna_feat = feats.front().second;

& feat = *feat_iter->second;

( ; obj_iter; ++obj_iter) {

(obj_iter->IsSetType() &&

obj_iter->GetType().IsStr() &&

obj_iter->GetType().GetStr() ==

) {

prot_id_str = obj_iter->GetField(

)

.GetData().GetStr();

vector<CSeq_id_Handle> ids = scope.

(prot_id);

(vector<CSeq_id_Handle>, id_iter, ids) {

(product_id.

(*id_iter->GetSeqId())) {

mrna_feat.

(&feat);

(exception&) {

& mrna = *feat_iter->second;

( ; other_iter && !mrna_feat; ++other_iter) {

( !prot_handle ) {

(prot_handle.

(product_id)) {

matching_feats.push_back(*feat_iter);

( !matching_feats.empty() ) {

feats.swap(matching_feats);

( feats.size() == 1 ) {

mrna_feat = feats.front().second;

(exception&) {

transcript_id = cds_feat.

(

);

( !transcript_id.empty() ) {

(vector<TFeatScore>, feat_iter, feats) {

& feat = *feat_iter->second;

other_transcript_id =

(transcript_id == other_transcript_id) {

mrna_feat.

(&feat);

mrna_feat = feats.back().second;

mrna_feat = feats.front().second;

unique_ptr<CFeat_CI> &feat_ci,

feat_ci, circular_length, range, loc, sel, scope, strand);

( bioseq_handle ) {

feat_ci.reset(

(bioseq_handle, range, strand, sel));

feat_ci.reset(

(scope, loc, sel));

&shouldContinueToNextIteration,

&revert_locations_this_iteration,

cleaned_loc_this_iteration, candidate_feat_loc,

overlap_type_this_iteration,

revert_locations_this_iteration,

bioseq_handle, feat, circular_length, annot_overlap_type);

cleaned_loc, candidate_feat_loc,

scope, sel, circular_length);

unique_ptr<CGetOverlappingFeaturesPlugin> cds_plugin(

feats, scope, opts, cds_plugin.get());

(feats.size() < 2) {

(feats.size() == 1) {

cds_feat = feats.front().second;

( ; obj_iter; ++obj_iter) {

(obj_iter->IsSetType() &&

obj_iter->GetType().IsStr() &&

obj_iter->GetType().GetStr() ==

) {

prot_id_str = obj_iter->GetField(

).GetData().GetStr();

( !prot_id_str.empty() ) {

vector<CSeq_id_Handle> ids = scope.

(prot_id);

& feat = *feat_iter->second;

(vector<CSeq_id_Handle>, id_iter, ids) {

(

.Match(*id_iter->GetSeqId())) {

cds_feat.

(&feat);

(exception&) {

& mrna_product =

( ; iter; ++iter) {

( !protein_id ) {

TFeatScores::const_iterator feat_iter = feats.begin();

TFeatScores::const_iterator feat_end = feats.end();

( ; feat_iter != feat_end && !cds_feat; ++feat_iter) {

& cds = *feat_iter->second;

( !prot_handle ) {

(prot_handle.

(*protein_id)) {

cds_feat.

(&cds);

( exception& ) {

transcript_id = mrna_feat.

(

);

( !transcript_id.empty() ) {

& feat = *feat_iter->second;

other_transcript_id =

(transcript_id == other_transcript_id) {

cds_feat.

(&feat);

cds_feat = feats.back().second;

cds_feat = feats.front().second;

feats, scope, opts, plugin );

(feats.size() < 2) {

(feats.size() == 1) {

gene_feat = feats.front().second;

& feat = *feat_it->second;

other_ref_str;

other_ref.

(&other_ref_str);

(ref_str == other_ref_str) {

((*dbxref)->GetDb() ==

||

(*dbxref)->GetDb() ==

) {

gene_id = (*dbxref)->GetTag().GetId();

& feat = *feat_it->second;

& db = (*dbxref)->GetDb();

((db ==

|| db ==

) &&

(*dbxref)->GetTag().GetId() == gene_id) {

gene_feat = feats.back().second;

gene_feat = feats.front().second;

feats, scope, opts, plugin );

(feats.size() < 2) {

(feats.size() == 1) {

feat_ref = feats.front().second;

& feat = *feat_it->second;

other_ref_str;

other_ref.

(&other_ref_str);

(ref_str == other_ref_str) {

feat_ref = feats.front().second;

(feat_it.

() == 0) {

( ; feat_it; ++feat_it) {

other_ref_str;

other_ref->

(&other_ref_str);

(other_ref_str != ref_str) {

mrna_feats.push_back(feat_ref);

((*dbxref)->GetDb() ==

||

(*dbxref)->GetDb() ==

) {

gene_id = (*dbxref)->GetTag().GetId();

( ; feat_it; ++feat_it) {

(((*dbxref)->GetDb() ==

||

(*dbxref)->GetDb() ==

) &&

(*dbxref)->GetTag().GetId() == gene_id) {

mrna_feats.push_back(ref);

scope, opts, plugin );

mrna_feats.push_back(feat);

list< CConstRef<CSeq_feat> > mrna_feats;

(mrna_feats.size()) {

cds_feats.push_back(cds);

scope, opts, plugin );

cds_feats.push_back(feat);

(feat_type) {

overlap_type, scope, opts, plugin );

overlap_type, scope, opts, plugin );

overlap_type, scope, opts, plugin );

(feat.

(), feat_type, overlap_type, scope, opts, plugin );

(feat.

(), subtype, overlap_type, scope, opts, plugin );

(

.IsLocal() ) {

( obj_id.

() ) {

local_id = obj_id.

();

( feat_handle ) {

&

.GetOriginalFeature();

m_Flags(fInstantiateGaps | fAssembleParts | fEnableGI),

m_GapMode(eGM_letters)

m_Gen.reset(

sequence::CDeflineGenerator);

loc2.

().Assign(*it->GetSeqId());

& custom_title)

(! desc.

())

;

(! oi.

())

;

& sid = **id_itr;

(sid.

()) {

& db = dbtag.

();

((*id)->IsGi()) {

(best_id->

())

hide_prefix =

;

(

& pId : bioseq.

()) {

(pId->IsGeneral()) {

(pId->IsGenbank()) {

(pAccession || pGnlId);

hide_prefix =

;

(gi_id, best_id, hide_prefix, bioseq);

pair<TSeq_id_HandleSet::iterator, bool> p

+ (*id)->AsFastaString()

+

);

c

-

-

s name is misleading, as it actually

(ms_it != masking_state.begin());

prev_state = prev_it->second;

ms_it = masking_state.insert(ms_it,

);

(++ms_it != masking_state.end() && ms_it->first < to) {

prev_state = ms_it->second;

ms_it->second |= eHardMask;

(ms_it == masking_state.end() || ms_it->first != to) {

& masking_state)

current_state = 0;

alt_gap_str = uc_hard_mask_str;

(rem_state == 0) {

current_state = ms_it->second;

(++ms_it == masking_state.

()) {

rem_state = ms_it->first - it.

();

<<

<< gap_size;

<<

;

<<

<< gap_size;

pGapLiteral->GetSeq_data().GetGap();

sGapModText =

( ! sGapModText.empty() ) {

<<

<< sGapModText;

(rem_gap >= rem_line) {

rem_gap -= rem_line;

rem_line -= rem_gap;

(rem_state >= gap_size) {

rem_state -= gap_size;

(++ms_it != masking_state.

()

&& ms_it->first < it.

()) {

current_state = ms_it->second;

(ms_it == masking_state.

()) {

rem_state = ms_it->first - it.

();

rem_state -=

;

ptr = (current_state &

) ? lc_hard_mask_str.

()

: uc_hard_mask_str.

();

}

(current_state &

) {

lc_buffer.assign(ptr,

);

ptr = lc_buffer.data();

(

>= rem_line ) {

vector<CTSE_Handle> used_tses;

+

);

(entry.

()) {

no_scope,

& custom_title )

is_raw =

;

<< sPrefix <<

<<

<<

;

& gap_type = out_gap_info.

;

vector<string> & gap_linkage_evidences =

gap_linkage_evidences.clear();

need_evidence =

;

( seq_gap.

() ) {

gap_type =

;

need_evidence = is_linkage;

gap_type =

;

need_evidence =

;

gap_type = ( is_linkage ?

:

);

need_evidence = is_linkage;

gap_type =

;

gap_type =

;

gap_type =

;

gap_type =

;

gap_type = ( is_linkage ?

:

);

need_evidence = is_linkage;

gap_type =

;

gap_type =

;

need_evidence = is_linkage;

gap_type =

;

need_evidence = is_linkage;

gap_type =

;

gap_type =

+

( evidence.

() ) {

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

);

gap_linkage_evidences.push_back(

+

( need_evidence && gap_linkage_evidences.empty() ) {

gap_linkage_evidences.push_back(

);

}

( ! need_evidence && ! gap_linkage_evidences.empty() ) {

gap_linkage_evidences.clear();

<

Container>

is_5prime_complete,

is_3prime_complete,

remove_trailing_X,

usable_size = seq.size() > frame ? seq.size() - frame : 0;

= usable_size % 3;

.reserve((usable_size + 2) / 3);

start_state = 0;

Container::const_iterator start = seq.begin();

(

= 0;

< frame; ++

) {

length = usable_size / 3;

check_start = (is_5prime_complete && frame == 0);

first_time =

;

(

= 0;

< length; ++

) {

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

start_state =

;

(first_time && check_start) {

.append(1, aa);

.append(1, aa);

first_time =

;

(k = 0; k <

; ++k, ++start) {

(; k < 3; ++k) {

start_state =

;

(first_time && check_start) {

.append(1, aa);

}

(c !=

) {

.append(1, aa);

( aa !=

&& include_stop && (!

) &&

.size() > 0 && is_3prime_complete ) {

(alt_start && is_5prime_complete) {

*alt_start =

;

( !include_stop ) {

(sz != string::npos) {

(remove_trailing_X) {

(sz =

.size(); sz > 0 &&

[sz - 1] ==

; --sz) {

(

->SetInst().SetExt().SetDelta().Set().empty()

||

->GetInst().GetExt().GetDelta().Get().back()->GetLiteral().GetSeq_data().IsGap()) {

seg->SetLiteral().SetLength(0);

->SetInst().SetExt().SetDelta().Set().push_back(seg);

(residue ==

|| residue ==

) {

(

->IsLiteral() &&

->GetLiteral().IsSetSeq_data() &&

->GetLiteral().GetSeq_data().IsIupacaa()) {

current =

->GetLiteral().GetSeq_data().GetIupacaa().Get();

->SetLiteral().SetSeq_data().SetNcbieaa().Set(current);

->SetLiteral().SetSeq_data().SetNcbieaa().Set().append(1, residue);

}

(

->IsLiteral() &&

->GetLiteral().IsSetSeq_data() &&

->GetLiteral().GetSeq_data().IsNcbieaa()) {

->SetLiteral().SetSeq_data().SetNcbieaa().Set().append(1, residue);

->SetLiteral().SetSeq_data().SetIupacaa().Set().append(1, residue);

->SetLiteral().SetLength(

+ 1);

(

->SetInst().SetExt().SetDelta().Set().empty()) {

new_seg->SetLiteral().SetLength(add_len);

(unknown_length) {

->SetInst().SetExt().SetDelta().Set().push_back(new_seg);

(

->SetLiteral().GetSeq_data().IsGap()

&& ((unknown_length &&

->SetLiteral().IsSetFuzz())

|| (!unknown_length && !

->SetLiteral().IsSetFuzz()))) {

=

->GetInst().GetExt().GetDelta().Get().back()->GetLiteral().GetLength();

->SetInst().SetExt().SetDelta().Set().back()->SetLiteral().SetLength(

+ add_len);

new_seg->SetLiteral().SetLength(add_len);

(unknown_length) {

->SetInst().SetExt().SetDelta().Set().push_back(new_seg);

->SetInst().SetLength(0);

(

= 0;

< frame; ++

) {

length = usable_size / 3;

check_start = (is_5prime_complete && frame == 0);

first_time =

;

(

= 0;

< length; ++

) {

is_gap =

;

unknown_length =

;

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

(is_gap && !unknown_length) {

unknown_length =

;

(first_time && check_start) {

first_time =

;

is_gap =

;

unknown_length =

;

pos = (length * 3) + frame;

(k = 0; k <

; ++k, ++start) {

(is_gap && !unknown_length) {

unknown_length =

;

(; k < 3; ++k) {

(first_time && check_start) {

prot_len += (*seg_it)->GetLiteral().GetLength();

string::size_type j = seq_pos / 3;

CDelta_ext::Tdata::iterator seg_it =

->SetInst().SetExt().SetDelta().Set().begin();

string::size_type

= 0;

(seg_it !=

->SetInst().SetExt().SetDelta().Set().end()

&&

+ (*seg_it)->GetLiteral().GetLength() < j) {

+= (*seg_it)->GetLiteral().GetLength();

(seg_it !=

->SetInst().SetExt().SetDelta().Set().end()

&& !(*seg_it)->GetLiteral().GetSeq_data().IsGap()) {

((*seg_it)->GetLiteral().GetSeq_data().IsIupacaa()) {

(*seg_it)->SetLiteral().SetSeq_data().SetIupacaa().Set()[j -

] = c_aa.

();

(*seg_it)->SetLiteral().SetSeq_data().SetNcbieaa().Set()[j -

] = c_aa.

();

}

(j == prot_len) {

(!

->SetInst().SetExt().SetDelta().Set().empty())

end =

->SetInst().SetExt().SetDelta().Set().back();

(end && end->IsLiteral() && end->GetLiteral().IsSetSeq_data()) {

(end->GetLiteral().GetSeq_data().IsIupacaa()) {

& last_seg = end->SetLiteral().SetSeq_data().SetIupacaa().Set();

last_seg = last_seg.substr(0, last_seg.length() - 1);

end->SetLiteral().SetLength(

(last_seg.length()));

}

(end->GetLiteral().GetSeq_data().IsNcbieaa()) {

& last_seg = end->SetLiteral().SetSeq_data().SetNcbieaa().Set();

last_seg = last_seg.substr(0, last_seg.length() - 1);

end->SetLiteral().SetLength(

(last_seg.length()));

prot_len += (*seg_it)->GetLiteral().GetLength();

((*seg_it)->GetLiteral().IsSetSeq_data()

&& (*seg_it)->GetLiteral().GetSeq_data().IsNcbieaa()) {

current = (*seg_it)->GetLiteral().GetSeq_data().GetNcbieaa();

(

(current,

) == string::npos &&

(current,

) == string::npos) {

(*seg_it)->SetLiteral().SetSeq_data().SetIupacaa().Set(current);

->SetInst().SetLength(prot_len);

(

->GetInst().GetLength() == 0) {

}

(

->SetInst().SetExt().SetDelta().Set().size() == 1

&&

->SetInst().SetExt().SetDelta().Set().front()->IsLiteral()

&&

->SetInst().SetExt().SetDelta().Set().front()->GetLiteral().IsSetSeq_data()) {

(

->SetInst().SetExt().SetDelta().Set().front()->GetLiteral().GetSeq_data().IsIupacaa()) {

=

->SetInst().SetExt().SetDelta().Set().front()->GetLiteral().GetSeq_data().GetIupacaa().Get();

->SetInst().ResetExt();

->SetInst().SetSeq_data().SetIupacaa().Set(

);

}

(

->SetInst().SetExt().SetDelta().Set().front()->GetLiteral().GetSeq_data().IsNcbieaa()) {

=

->SetInst().SetExt().SetDelta().Set().front()->GetLiteral().GetSeq_data().GetNcbieaa().Get();

->SetInst().ResetExt();

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

);

(!protein || !protein->

() || !protein->

()) {

protein->

().ConvertDeltaToRaw();

remove_trailing_X,

is_5prime_complete,

is_3prime_complete)

is_5prime_complete, is_3prime_complete, include_stop, remove_trailing_X, alt_start);

!(

& fIs5PrimePartial),

!(

& fIs3PrimePartial),

!(

& fNoStop),

& fRemoveTrailingX,

remove_trailing_X,

is_5prime_complete,

is_3prime_complete)

is_5prime_complete, is_3prime_complete, include_stop, remove_trailing_X, alt_start);

!(

& fIs5PrimePartial),

!(

& fIs3PrimePartial),

!(

& fNoStop),

& fRemoveTrailingX,

remove_trailing_X,

include_stop, remove_trailing_X, alt_start);

remove_trailing_X,

include_stop, remove_trailing_X, alt_start);

remove_trailing_X,

frame = 0;

code_break_include_stop = include_stop;

code_break_include_stop =

;

code_break_include_stop, remove_trailing_X, alt_start);

string::size_type protlen =

.size();

string::size_type

= seq_pos / 3;

}

(

== protlen) {

( !include_stop ) {

(sz != string::npos) {

(

it = frame_map.

(); it != frame_map.

(); it++) {

tmp_cds->

().SetCdregion().SetFrame(it->first);

it->second.len =

.length();

((pos ==

.length() - 1) && (leftover == it->second.frame_offset)) {

it->second.has_final_stop =

;

}

(pos !=

) {

it->second.has_internal_stop =

;

it->second.has_start_m =

;

(frame_map[orig_frame].has_final_stop) {

(is_3complete && !is_5complete) {

(

it = frame_map.

(); it != frame_map.

(); it++) {

(it->second.has_final_stop) {

(is_5complete && !is_3complete) {

(

it = frame_map.

(); it != frame_map.

(); it++) {

(it->second.has_final_stop) {

(!frame_map[orig_frame].has_internal_stop) {

(

it = frame_map.

(); it != frame_map.

(); it++) {

(!it->second.has_internal_stop) {

best_frame = it->first;

ambiguous =

;

FindBestFrame(cds, scope, ambiguous);

remove_trailing_X,

include_stop, remove_trailing_X, alt_start);

remove_trailing_X,

include_stop, remove_trailing_X, alt_start);

: m_ParentLoc(&parent)

& cseqid = cit.GetSeq_id();

TRange0 crange = cit.GetRange();

(crange.IsWholeTo() && scope) {

TRange0 prange = pit.GetRange();

(prange.IsWholeTo() && scope) {

pos += prange.GetLength();

(crange.GetFrom() >= prange.GetFrom()) {

abs_from = crange.GetFrom();

fuzz_from = cit.GetFuzzFrom();

(abs_from == prange.GetFrom()) {

* pfuzz = pit.GetFuzzFrom();

->Assign(*fuzz_from);

->Subtract(*pfuzz, abs_from, abs_from);

(

->IsP_m() && !

->GetP_m() ) {

fuzz_from.

();

fuzz_from = pfuzz->

(abs_from);

abs_from = prange.GetFrom();

(crange.GetTo() <= prange.GetTo()) {

abs_to = crange.GetTo();

fuzz_to = cit.GetFuzzTo();

(abs_to == prange.GetTo()) {

* pfuzz = pit.GetFuzzTo();

->Assign(*fuzz_to);

->Subtract(*pfuzz, abs_to, abs_to);

(

->IsP_m() && !

->GetP_m() ) {

fuzz_to = pfuzz->

(abs_to);

abs_to = prange.GetTo();

(abs_from <= abs_to) {

sigma = pos + prange.GetTo();

intersection->SetFrom(sigma - abs_to);

intersection->SetTo (sigma - abs_from);

intersection->SetFuzz_to().AssignTranslated

(*fuzz_from, intersection->GetTo(), abs_from);

intersection->SetFuzz_to().Negate

(intersection->GetTo());

intersection->SetFuzz_from().AssignTranslated

(*fuzz_to, intersection->GetFrom(), abs_to);

intersection->SetFuzz_from().Negate

(intersection->GetFrom());

intersection->SetStrand(pstrand);

intersection->SetStrand(

(cstrand));

intersection->SetFrom(abs_from +

);

intersection->SetTo (abs_to +

);

intersection->SetFuzz_from().AssignTranslated

(*fuzz_from, intersection->GetFrom(), abs_from);

intersection->SetFuzz_to().AssignTranslated

(*fuzz_to, intersection->GetTo(), abs_to);

intersection->SetStrand(pstrand);

intersection->SetStrand(cstrand);

(

.back()->GetTo() == intersection->GetFrom() - 1

&& !

(intersection->GetStrand()) ) {

.back()->SetTo(intersection->GetTo());

(intersection->IsSetFuzz_to()) {

(intersection->SetFuzz_to());

}

(

.back()->GetFrom()

== intersection->GetTo() + 1

&&

(intersection->GetStrand())) {

.back()->SetFrom(intersection->GetFrom());

(intersection->IsSetFuzz_from()) {

(intersection->SetFuzz_from());

.back()->ResetFuzz_from();

pos += prange.GetLength();

((*it)->GetFrom() <= (*it)->GetTo());

pos = 0, start = (*it)->GetFrom();

keep_going =

;

TRange0 prange = pit.GetRange();

(prange.IsWholeTo() && scope) {

length = prange.GetLength();

(start >= pos && start < pos + length) {

sigma = pos + prange.GetTo();

from = sigma - (*it)->GetTo();

(from < prange.GetFrom() || from > sigma) {

from = prange.GetFrom();

keep_going =

;

( !(*it)->IsSetStrand()

strand = pit.GetStrand();

strand =

((*it)->GetStrand());

(from == prange.GetFrom()) {

fuzz_from = pit.GetFuzzFrom();

( !keep_going && (*it)->IsSetFuzz_to() ) {

->Assign(*fuzz_from);

->Subtract((*it)->GetFuzz_to(), from, (*it)->GetTo(),

(

->IsP_m() && !

->GetP_m() ) {

fuzz_from.

();

(to == prange.GetTo()) {

fuzz_to = pit.GetFuzzTo();

(start == (*it)->GetFrom()

&& (*it)->IsSetFuzz_from()) {

->Assign(*fuzz_to);

->Subtract((*it)->GetFuzz_from(), to,

(

->IsP_m() && !

->GetP_m() ) {

from = start +

;

to = (*it)->GetTo() +

;

(to > prange.GetTo()) {

to = prange.GetTo();

keep_going =

;

( !(*it)->IsSetStrand()

strand = pit.GetStrand();

strand = (*it)->GetStrand();

(from == prange.GetFrom()) {

fuzz_from = pit.GetFuzzFrom();

(start == (*it)->GetFrom()

&& (*it)->IsSetFuzz_from()) {

->Assign(*fuzz_from);

->Add((*it)->GetFuzz_from(), from,

->AssignTranslated((*it)->GetFuzz_from(), from,

(

->IsP_m() && !

->GetP_m() ) {

fuzz_from.

();

(to == prange.GetTo()) {

fuzz_to = pit.GetFuzzTo();

( !keep_going && (*it)->IsSetFuzz_to() ) {

->Assign(*fuzz_to);

->Add((*it)->GetFuzz_to(), to, (*it)->GetTo());

->AssignTranslated((*it)->GetFuzz_to(), to,

(

->IsP_m() && !

->GetP_m() ) {

&& (fuzz_from == fuzz_to

&& fuzz_from->

(*fuzz_to)))) {

point.

().Assign(*fuzz_from);

point.

().Assign(pit.GetSeq_id());

mix.

().push_back(loc);

ival.

().Assign(pit.GetSeq_id());

mix.

().push_back(loc);

start = pos + length;

<< start <<

<< total_length

<<

<<

);

<<

(mix.

().size()) {

m_Client(

), m_Flags(

), m_LongestPattern(0), m_Fsa(

)

(comp_it != sc_Complement.end()) ? comp_it->second :

;

.reserve(sequence.length());

string::const_reverse_iterator rend = sequence.rend();

(string::const_reverse_iterator rit = sequence.rbegin(); rit != rend; ++rit) {

(

& name,

& sequence,

pattern = sequence;

symmetric = (pattern ==

);

revcomp_cut_site =

(pattern.length()) - cut_site;

(

current_state,

(!

.IsPrimed()) {

next_state =

.GetNextState(current_state, ch);

(

.IsMatchFound(next_state)) {

(vector<TPatternInfo>, it,

.GetMatches(next_state)) {

start = position -

(it->GetSequence().length()) + 1;

(start < length) {

(

= 0;

< search_len; ++

) {

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

(

& name,

.reserve(pattern.length());

(

& sequence,

(pos < sequence.length()) {

(

= 0;

< 4; ++

) {

((

& expansion[

]) != 0) {

.AddWord(sequence, pat_info);

);

inst.

().SetDelta().Set().reverse();

((*it)->Which()) {

((*it)->GetLiteral().IsSetSeq_data()) {

(*it)->SetLoc(*flip);

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

LargeInt< 1 > revcomp(const LargeInt< 1 > &x, size_t sizeKmer)

User-defined methods of the data storage class.

bool IsReverse(ENa_strand s)

ENa_strand Reverse(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.

size_t GetSize(void) const

virtual void setUpFeatureIterator(CBioseq_Handle &bioseq_handle, unique_ptr< CFeat_CI > &feat_ci, TSeqPos circular_length, CRange< TSeqPos > &range, const CSeq_loc &loc, SAnnotSelector &sel, CScope &scope, ENa_strand &strand)

virtual void processMainLoop(bool &shouldContinueToNextIteration, CRef< CSeq_loc > &cleaned_loc_this_iteration, CRef< CSeq_loc > &candidate_feat_loc, EOverlapType &overlap_type_this_iteration, bool &revert_locations_this_iteration, CBioseq_Handle &bioseq_handle, const CMappedFeat &feat, TSeqPos circular_length, SAnnotSelector::EOverlapType annot_overlap_type)

CGetOverlappingFeaturesPlugin * m_PrevPlugin

virtual void processSAnnotSelector(SAnnotSelector &sel)

virtual void postProcessDiffAmount(Int8 &cur_diff, CRef< CSeq_loc > &cleaned_loc, CRef< CSeq_loc > &candidate_feat_loc, CScope &scope, SAnnotSelector &sel, TSeqPos circular_length)

virtual ~CCdsForMrnaPlugin()

CCdsForMrnaPlugin(CGetOverlappingFeaturesPlugin *prev_plugin)

virtual void processLoc(CBioseq_Handle &bioseq_handle, CRef< CSeq_loc > &loc, TSeqPos circular_length)

CTime AsCTime(CTime::ETimeZone tz=CTime::eLocal) const

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

static const CTrans_table & GetTransTable(int id)

void GetLabel(string *label) const

bool IsSuppressed(void) const

CRef< CInt_fuzz > Negative(TSeqPos n) const

@ eAmplify

go for the largest possible range

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Base class for all object manager exceptions.

Exceptions for objmgr/util library.

bool operator()(const pair< Int8, CConstRef< CSeq_feat > > &gene1, const pair< Int8, CConstRef< CSeq_feat > > &gene2)

COverlapPairLess(CScope *scope_arg)

ESubtype GetSubtype(void) const

static E_Choice GetTypeFromSubtype(ESubtype subtype)

Holds information associated with a pattern, such as the name of the restriction enzyme,...

Client interface: ================== A class that uses the SeqSearch facility should implement the Cl...

SeqVector related exceptions.

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

const CGene_ref * GetGeneXref(void) const

See related function in util/feature.hpp.

static bool IsAa(EMol mol)

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

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

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

TBase::const_iterator const_iterator

TSeq_feat_Handles GetGenesWithLocus(const string &locus, bool tag) const

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

vector< CSeq_feat_Handle > TSeq_feat_Handles

CSeq_feat_Handle GetFeatureWithId(CSeqFeatData::E_Choice type, TFeatureIdInt id) const

CScope & GetScope(void) const

Returns scope.

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

char GetStartResidue(int state) const

char GetCodonResidue(int state) const

bool IsAltStart(int state) const

static int NextCodonState(int state, unsigned char ch)

char GetStopResidue(int state) const

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

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

container_type::value_type value_type

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

API (CDeflineGenerator) for computing sequences' titles ("definitions").

std::ofstream out("events_result.xml")

main entry point for tests

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

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

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

static const struct type types[]

static const char location[]

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

#define FOR_EACH_USERFIELD_ON_USEROBJECT(Itr, Var)

FOR_EACH_USERFIELD_ON_USEROBJECT EDIT_EACH_USERFIELD_ON_USEROBJECT.

void reset(element_type *p=0, EOwnership ownership=eTakeOwnership)

Reset will delete the old pointer (if owned), set content to the new value, and assume the ownership ...

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.

element_type * get(void) const

Get pointer.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

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

@ ePositive

Value is positive.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

#define NCBI_THROW_FMT(exception_class, err_code, message)

The same as NCBI_THROW but with message processed as output to ostream.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

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

Set object to copy of another one.

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

Check if both objects contain the same values.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

CConstRef< CSeq_id > GetSeqId(void) const

void Reset(void)

Reset the handle (remove seq-id reference)

static CSeq_id_Handle GetGiHandle(TGi gi)

Faster way to create a handle for a gi.

E_SIC

Compare return values.

virtual void WriteAsFasta(ostream &out) const

Implement serializable interface.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static int WorstRank(const CRef< CSeq_id > &id)

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

static int BestRank(const CRef< CSeq_id > &id)

CSeq_id::E_Choice Which(void) const

static int FastaNARank(const CRef< CSeq_id > &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

static bool PreferAccessionOverGi(void)

Check if the option to prefer accession.version over GI is enabled (SeqId/PreferAccessionOverGi or SE...

static bool AvoidGi(void)

Check if the option to avoid GI ids is enabled (SeqId/AvoidGi or SEQ_ID_AVOID_GI).

E_SIC Compare(const CSeq_id &sid2) const

Compare() - more general.

static int FastaAARank(const CRef< CSeq_id > &id)

@ e_NO

different SeqId types-can't compare

@ e_YES

SeqIds compared, but are different.

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.

void FlipStrand(void)

Flip the strand (e.g. plus to minus)

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

Override Assign() to incorporate cache invalidation.

EOpFlags

CSeq_loc operations.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool CheckId(const CSeq_id *&id, bool may_throw=true) const

check that the 'id' field in all parts of the location is the same as the specifies id.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

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

const CSeq_id * GetId(void) const

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

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

void GetLabel(string *label) const

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

void SetStrand(ENa_strand strand)

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

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

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...

Int8 TestForOverlapEx(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, CScope *scope=0, TOverlapFlags flags=fOverlap_Default)

Updated version of TestForOverlap64().

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.

Int8 TestForOverlap64(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSeqPos circular_len=kInvalidSeqPos, CScope *scope=0)

64-bit version of TestForOverlap() Check if the two locations have ovarlap of a given type.

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

Merge ranges in the seq-loc.

bool IsOneBioseq(const CSeq_loc &loc, CScope *scope)

Returns true if all embedded CSeq_ids represent the same CBioseq, else false.

int TestForOverlap(const CSeq_loc &loc1, const CSeq_loc &loc2, EOverlapType type, TSeqPos circular_len=kInvalidSeqPos, CScope *scope=0)

Calls TestForOverlap64() and if the result is greater than kMax_Int truncates it to kMax_Int.

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.

CSeq_loc * SeqLocRevCmpl(const CSeq_loc &loc, CScope *scope)

Get reverse complement of the seq-loc (?)

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.

@ eOverlap_SubsetRev

1st is a subset of 2nd ranges

@ eOverlap_CheckIntervals

2nd is a subset of 1st with matching boundaries

@ eOverlap_Contains

2nd contains 1st extremes

@ eOverlap_CheckIntRev

1st is a subset of 2nd with matching boundaries

@ eOverlap_Simple

any overlap of extremes

@ eOverlap_Interval

at least one pair of intervals must overlap

@ eOverlap_Contained

2nd contained within 1st extremes

@ eOverlap_Subset

2nd is a subset of 1st ranges

@ eContains

First CSeq_loc contains second.

@ eSame

CSeq_locs contain each other.

@ fOverlap_IgnoreTopology

Ignore sequence topology (circularity)

@ fOverlap_Default

Enable multi-id, multi-strand, check topology.

@ eOffset_FromStart

For positive-orientation strands, start = left and end = right; for reverse-orientation strands,...

void AddNucleotidePattern(const string &name, const string &sequence, Int2 cut_site, TSearchFlags flags=fNoFlags)

Add nucleotide pattern or restriction site to sequence search.

CRef< CSeq_loc > ProductToSource(const CSeq_feat &feat, const CSeq_loc &prod_loc, TP2SFlags flags, CScope *scope)

virtual void processSAnnotSelector(SAnnotSelector &sel)=0

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

CTextFsm< TPatternInfo > m_Fsa

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

virtual void setUpFeatureIterator(CBioseq_Handle &bioseq_handle, unique_ptr< CFeat_CI > &feat_ci, TSeqPos circular_length, CRange< TSeqPos > &range, const CSeq_loc &loc, SAnnotSelector &sel, CScope &scope, ENa_strand &strand)=0

void SetMask(EMaskType type, CConstRef< CSeq_loc > location)

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

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

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

CBioseq_Handle GetBioseqFromSeqLoc(const CSeq_loc &loc, CScope &scope, CScope::EGetBioseqFlag flag)

Retrieve the Bioseq Handle from a location.

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

virtual void processLoc(CBioseq_Handle &bioseq_handle, CRef< CSeq_loc > &loc, TSeqPos circular_length)=0

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

CConstRef< CSeq_loc > m_HardMask

void x_WriteSequence(const CSeqVector &vec, const TMSMap &masking_state)

vector< CRef< TRange > > TRanges

string GetProteinName(const CBioseq_Handle &seq)

Return protein name from corresponding Prot-ref feature.

virtual bool SkipBioseq(const CBioseq &)

Used only by Write(CSeq_entry[_Handle], ...); permissive by default.

CConstRef< CSeq_feat > GetBestCdsForMrna(const CSeq_feat &mrna_feat, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin)

void GetOrg_refForProduct(const CBioseq_Handle &bsh, const COrg_ref *pOrgRef)

static bool ChangeDeltaProteinToRawProtein(CRef< CBioseq > protein)

void x_ExpandPattern(string &sequence, string &buffer, size_t pos, TPatternInfo &pat_info, TSearchFlags flags)

TGi GetGiForAccession(const string &acc, CScope &scope, EGetIdType flags)

Given an accession string retrieve the GI id.

string GetAccessionForId(const objects::CSeq_id &id, CScope &scope, EAccessionVersion use_version, EGetIdType flags)

Retrieve the accession string for a Seq-id.

ETranslationLengthProblemOptions

CConstRef< CSeq_feat > GetSourceFeatForProduct(const CBioseq_Handle &bsh)

vector< string > gap_linkage_evidences

A vector representing the linkage-evidences of the gap.

virtual void WriteTitle(const CBioseq_Handle &handle, const CSeq_loc *location=0, const string &custom_title=kEmptyStr)

CConstRef< CSeq_loc > m_ParentLoc

virtual bool OnPatternFound(const TPatternInfo &pat_info, TSeqPos pos)=0

CRef< CSeq_loc > Resolve(CScope *scope=0, TFlags flags=0) const

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

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

void x_StorePattern(TPatternInfo &pat_info, string &sequence)

ETransSplicing

Convenience functions for popular overlapping types.

pair< Int8, CConstRef< CSeq_feat > > TFeatScore

Storage for features and scores.

CConstRef< CSeq_feat > GetGeneForFeature(const CSeq_feat &feat, CScope &scope)

Finds gene for feature, but obeys SeqFeatXref directives.

TSeq_id_HandleSet m_PreviousWholeIds

CConstRef< CSeq_feat > GetBestGeneForMrna(const CSeq_feat &mrna_feat, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin)

virtual void x_WriteSeqIds(const CBioseq &bioseq, const CSeq_loc *location)

CConstRef< CSeq_feat > GetBestMrnaForCds(const CSeq_feat &cds_feat, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin)

virtual const char * GetErrCodeString(void) const override

string m_Sequence

user defined name

bool x_IsAllowMismatch(TSearchFlags flags) const

void SetWidth(TSeqPos width)

TTaxId GetTaxIdForProduct(const CBioseq_Handle &bsh)

CConstRef< CSeq_feat > GetBestOverlapForSNP(const CSeq_feat &snp_feat, CSeqFeatData::E_Choice type, CScope &scope, bool search_both_strands)

Get the best overlapping feature for a SNP (variation) feature.

~CSeqSearch(void)

destructor

CConstRef< CSeq_loc > m_SoftMask

EMaskType

Which residues to mask out in subsequent output.

const CBioSource * GetBioSource(const CBioseq &bioseq)

Retrieve the BioSource object for a given bioseq handle.

TGi GetGiForId(const objects::CSeq_id &id, CScope &scope, EGetIdType flags)

Given a Seq-id retrieve the corresponding GI.

void x_AddNucleotidePattern(const string &name, string &pattern, Int2 cut_site, ENa_strand strand, TSearchFlags flags)

virtual void WriteSequence(const CBioseq_Handle &handle, const CSeq_loc *location=0, CSeq_loc::EOpFlags merge_flags=CSeq_loc::fMerge_AbuttingOnly)

virtual void postProcessDiffAmount(Int8 &cur_diff, CRef< CSeq_loc > &cleaned_loc_this_iteration, CRef< CSeq_loc > &candidate_feat_loc, CScope &scope, SAnnotSelector &sel, TSeqPos circular_length)=0

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

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

CBioseq_Handle GetParentForPart(const CBioseq_Handle &part)

Get the parent bioseq for a part of a segmented bioseq.

CConstRef< CSeq_loc > GetMask(EMaskType type) const

CSeqSearch(IClient *client=0, TSearchFlags flags=fNoFlags)

constructors

CConstRef< CSeq_id > FindLatestSequence(const CSeq_id &id, CScope &scope)

Given a seq-id check its replace history and try to find the latest revision.

string GetAccessionForGi(TGi gi, CScope &scope, EAccessionVersion use_version, EGetIdType flags)

Retrieve the accession for a given GI.

const CMolInfo * GetMolInfo(const CBioseq &bioseq)

Retrieve the MolInfo object for a given bioseq handle.

virtual void x_WriteSeqTitle(const CBioseq_Handle &handle, const string &custom_title)

void Search(const CBioseq_Handle &seq)

Search the sequence for patterns.

void GetMrnasForGene(const CSeq_feat &gene_feat, CScope &scope, list< CConstRef< CSeq_feat > > &mrna_feats, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin)

CRef< CSeq_loc > SourceToProduct(const CSeq_feat &feat, const CSeq_loc &source_loc, TS2PFlags flags, CScope *scope, int *frame)

const CSeq_feat * GetPROTForProduct(const CBioseq &product, CScope *scope)

Get the mature peptide feature of a protein.

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

Find "best" frame for a coding region.

CSeq_id_Handle GetId(const CBioseq &seq, EGetIdType type)

Return a selected ID type from a Bioseq Arguments (except 'seq') and behavior is the same as of GetId...

CConstRef< CSeq_feat > GetBestGeneForCds(const CSeq_feat &cds_feat, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin)

const COrg_ref * GetOrg_refOrNull(const CBioseq_Handle &handle)

Return the pointer to org-ref associated with a given sequence or null if there is no org-ref associa...

void x_GetMaskingStates(TMSMap &masking_states, const CSeq_id *base_seq_id, const CSeq_loc *location, CScope *scope)

string gap_type

String representing the gap type.

virtual void processMainLoop(bool &shouldContinueToNextIteration, CRef< CSeq_loc > &cleaned_loc_this_iteration, CRef< CSeq_loc > &candidate_feat_loc, EOverlapType &overlap_type_this_iteration, bool &revert_locations_this_iteration, CBioseq_Handle &bioseq_handle, const CMappedFeat &feat, TSeqPos circular_length, SAnnotSelector::EOverlapType annot_overlap_type)=0

CMappedFeat GetMappedCDSForProduct(const CBioseq_Handle &bsh)

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.

virtual void x_GetBestId(CConstRef< CSeq_id > &gi_id, CConstRef< CSeq_id > &best_id, bool &hide_prefix, const CBioseq &bioseq)

const CBioSource * GetBioSourceForBioseq(const CBioseq_Handle &bsh)

Find a BioSource for the given Bioseq: If it's a protein then look for the source feature of the prod...

static void TranslateCdregion(string &prot, const CBioseq_Handle &bsh, const CSeq_loc &loc, const CCdregion &cdr, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=0, ETranslationLengthProblemOptions options=eThrowException)

translation coding region into ncbieaa protein sequence

vector< TFeatScore > TFeatScores

virtual void x_WriteBuffer(const char *buf, unsigned int count)

const CSeq_feat * GetmRNAForProduct(const CBioseq &product, CScope *scope)

Get the encoding mRNA feature of a given mRNA (cDNA) bioseq.

EGapMode

How to represent gaps with fInstantiateGaps enabled, as it is by default.

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

bool x_IsExpandPattern(TSearchFlags flags) const

CConstRef< CSeq_feat > GetBestOverlappingFeat(const CSeq_loc &loc, CSeqFeatData::E_Choice feat_type, EOverlapType overlap_type, CScope &scope, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin)

See the note above on 'overlap_type' meaning.

void GetCdssForGene(const CSeq_feat &gene_feat, CScope &scope, list< CConstRef< CSeq_feat > > &cds_feats, TBestFeatOpts opts, CGetOverlappingFeaturesPlugin *plugin)

void ReverseComplement(CSeq_inst &inst, CScope *scope)

Reverse complement a Bioseq in place.

CMappedFeat GetMappedmRNAForProduct(const CBioseq_Handle &bsh)

unsigned int TSearchFlags

binary OR of ESearchFlag

void WriteAllModsAsFasta(CNcbiOstream &out) const

This will write the modifiers in FASTA format.

virtual void x_WriteAsFasta(const CBioseq &bioseq)

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

Get the encoding nucleotide sequnce of a protein.

const COrg_ref & GetOrg_ref(const CBioseq_Handle &handle)

Return the org-ref associated with a given sequence.

bool x_IsJustTopStrand(TSearchFlags flags) const

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, CGetOverlappingFeaturesPlugin *plugin)

Find all features overlapping the location.

static void GetGapModText(const CSeq_gap &seq_gap, SGapModText &out_gap_mod_text)

Given a CSeq_gap object, this outputs the Gap information.

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.

void x_AddPattern(TPatternInfo &pat_info, string &sequence, TSearchFlags flags)

const COrg_ref * GetOrg_refForBioseq(const CBioseq_Handle &bsh)

Find an Org-ref for the given Bioseq: If it's a protein then look on the source feature of the produc...

int TFlags

binary OR of EFlags

SRelLoc(const CSeq_loc &parent, const CSeq_loc &child, CScope *scope=0, TFlags flags=0)

Beware: treats locations corresponding to different sequences as disjoint, even if one is actually a ...

@ eWithAccessionVersion

accession.version (when possible)

@ fS2P_NoMerge

don't merge adjacent intervals on the product

@ fS2P_AllowTer

map the termination codon as a legal location

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

@ eGetId_Seq_id_FastaNARank

use CSeq_id::FastaNARank() as the scoring function

@ eGetId_Seq_id_WorstRank

use CSeq_id::WorstRank() as the scoring function

@ eGetId_ThrowOnError

Throw exception on errors. If not set, an empty value is returned.

@ eGetId_ForceAcc

return only an accession based seq-id

@ eGetId_ForceGi

return only a gi-based seq-id

@ eGetId_Seq_id_Score

use CSeq_id::Score() as the scoring function

@ eGetId_Seq_id_FastaAARank

use CSeq_id::FastaAARank() as the scoring function

@ eGetId_Seq_id_BestRank

use CSeq_id::BestRank() as the scoring function

@ eGetId_VerifyId

Check if the seq-id is present in the scope.

@ eGetId_TypeMask

Mask for requested id type.

@ eTransSplicing_Auto

Ignore overlap strand if the source location has mixed/both strand.

@ fInstantiateGaps

honor specifed gap mode; on by default

@ fHideGenBankPrefix

Hide gb| prefix for genbank only seq_id's.

@ fShowGapsOfSizeZero

Use this to show gaps of size zero as a lone hyphen at the end of a line.

@ fShowGnlAndAcc

Show general id and accession in the defline.

@ fKeepUnknGapNomLen

Keep unknown gap's nominal length. That is, when a gap has an unknown length but nominal length,...

@ fSuppressRange

never include location details in defline

@ fShowGapModifiers

show gap key-value pair modifiers (e.g. "[linkage-evidence=map;strobe]"). Only works if gap mode is e...

@ fNoDupCheck

skip check for duplicate sequence IDs

@ fEnableGI

Use this flag to enable GI output in the defline.

@ fReverseStrand

flip the (implicit) location

@ fAssembleParts

assemble FAR delta sequences; on by dflt

@ eHardMask

write as N for nucleotides, X for peptides

@ eSoftMask

write as lowercase rather than uppercase

@ fP2S_Extend

if hitting ends, extend to include partial codons

@ eGM_letters

Multiple inline Ns or Xs as appropriate (default).

@ eGM_count

>?N or >?unk100, as appropriate.

@ eGM_dashes

Multiple inline dashes.

@ eGM_one_dash

A single dash, followed by a line break.

@ fBestFeat_NoExpensive

don't perform any expensive tests, such as ones that require fetching additional sequences

@ fBestFeat_FavorLonger

favor longer features over shorter features

@ fBestFeat_StrictMatch

requires explicit association, rather than analysis based on overlaps

@ fBestFeat_IgnoreStrand

Pay no attention to strands when finding the best feat.

@ fNoMerge

don't merge adjacent intervals

TIds GetIds(const CSeq_id &id, TGetFlags flags=0)

Get "native" bioseq ids without filtering and matching.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

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

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TGi GetGi(const CSeq_id_Handle &idh, TGetFlags flags=0)

Get GI of a sequence Returns ZERO_GI if the sequence is not found or if it doesn't have GI.

vector< CSeq_id_Handle > TIds

@ eGetBioseq_Loaded

Search in all loaded TSEs in the scope.

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

bool IsSetInst_Seq_data(void) const

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

bool IsSetDbxref(void) const

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

CSeq_id_Handle GetAccessSeq_id_Handle(void) const

Get any CSeq_id_Handle handle that can be used to access this bioseq Use GetSeq_id_Handle() if it's n...

TSeqPos GetBioseqLength(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.

bool IsProtein(void) const

TInst_Topology GetInst_Topology(void) const

bool IsSetInst(void) const

void Reset(void)

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

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_entry_Handle GetExactComplexityLevel(CBioseq_set::EClass cls) const

Return level with exact complexity, or empty handle if not found.

const CSeq_feat::TDbxref & GetDbxref(void) const

const CSeqMap & GetSeqMap(void) const

Get sequence map.

bool IsSetInst_Topology(void) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const TId & GetId(void) const

bool IsSynonym(const CSeq_id &id) const

Check if this id can be used to obtain this bioseq handle.

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

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

CSeqVector_CI & SetPos(TSeqPos pos)

const char * GetBufferPtr(void) const

Get pointer to current char in the buffer.

ENa_strand GetStrand(void) const

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetResolveTSE(void)

SetResolveTSE() is equivalent to SetResolveMethod(eResolve_TSE).

SAnnotSelector & SetFeatType(TFeatType type)

Set feature type (also set annotation type to feat)

SSeqMapSelector & SetLinkUsedTSE(bool link=true)

TSeqPos SkipGap(void)

skip current gap forward returns number of skipped gap symbols does nothing and returns 0 if current ...

TSeqPos GetPos(void) const

const CSeq_loc & GetLocation(void) const

SAnnotSelector & SetByProduct(bool byProduct=true)

Set flag indicating if the features should be searched by their product rather than location.

SAnnotSelector & SetOverlapType(EOverlapType overlap_type)

Set overlap type.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

TSeqPos GetGapSizeForward(void) const

returns number of gap symbols ahead including current symbol returns 0 if current position is not in ...

SAnnotSelector & SetAdaptiveDepth(bool value=true)

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

SAnnotSelector & SetSearchUnresolved(void)

EOverlapType

Flag to indicate location overlapping method.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

TSeqPos GetBufferSize(void) const

Get number of chars from current position to the current buffer end.

const CSeq_loc & GetProduct(void) const

CSeqMap::ESegmentType GetType(void) const

bool HasZeroGapBefore(void)

true if there is zero-length gap before current position

bool IsUnknownLength(void) const

return true if current segment is a gap of unknown length

SAnnotSelector & SetOverlapIntervals(void)

Check overlapping of individual intervals.

void SetStrand(ENa_strand strand)

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

SAnnotSelector & SetIgnoreStrand(bool value=true)

Ignore strand when testing for range overlap.

CConstRef< CSeq_literal > GetRefGapLiteral(void) const

return CSeq_literal with gap data, or null if either the segment is not a gap, or an unspecified gap

const CSeqMap_CI & GetCurrentSeqMap_CI() const

@ eOverlap_Intervals

default - overlapping of individual intervals

@ eOverlap_TotalRange

overlapping of total ranges only

bool IsInGap(TSeqPos pos) const

true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe,...

const CSeqMap & GetSeqMap(void) const

bool IsProtein(void) const

void SetCoding(TCoding coding)

bool CanResolveRange(CScope *scope, const SSeqMapSelector &sel) const

const_iterator begin(void) const

TResidue GetGapChar(ECaseConversion case_cvt=eCaseConversion_none) const

Return gap symbol corresponding to the selected coding.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int16_t Int2

2-byte (16-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

position_type GetLength(void) const

TThisType & SetToOpen(position_type toOpen)

position_type GetToOpen(void) const

static TThisType GetEmpty(void)

static TThisType GetWhole(void)

#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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

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).

CTempString & assign(const char *src_str, size_type len)

Assign new values to the content of the a string.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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.

const char * data(void) const

Return a pointer to the array represented.

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 string & ToUpper(string &str)

Convert string to upper case – string& version.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

ESign GetSign(void) const

Get sign of time span.

CTimeSpan DiffTimeSpan(const CTime &t) const

Difference in nanoseconds from specified time.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

static const char label[]

const TOrg & GetOrg(void) const

Get the Org member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

bool IsSetPseudo(void) const

pseudogene Check if a value has been assigned to Pseudo data member.

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.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetDb(void) const

name of database or system Check if a value has been assigned to Db data member.

bool IsSetType(void) const

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

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

const TDb & GetDb(void) const

Get the Db member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

bool IsSetData(void) const

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

TId GetId(void) const

Get the variant data.

vector< CRef< CDbtag > > TDbxref

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.

bool IsSetCode(void) const

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

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.

const TLoc & GetLoc(void) const

Get the Loc member data.

const TQual & GetQual(void) const

Get the Qual member data.

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.

E_Choice

Choice variants.

const TId & GetId(void) const

Get the Id member data.

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.

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

bool IsNcbieaa(void) const

Check if variant Ncbieaa is selected.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

const TAa & GetAa(void) const

Get the Aa member data.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

const TProduct & GetProduct(void) const

Get the Product member data.

TNcbieaa GetNcbieaa(void) const

Get the variant data.

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TGene & GetGene(void) const

Get the variant data.

bool IsSetId(void) const

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

TExcept GetExcept(void) const

Get the Except member data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

vector< CRef< CGb_qual > > TQual

bool IsSetDbxref(void) const

support for xref to other databases Check if a value has been assigned to Dbxref 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 IsSetCode_break(void) const

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

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.

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

void SetTo(TTo value)

Assign a value to To data member.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetAccession(void) const

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

bool IsMix(void) const

Check if variant Mix is selected.

ENa_strand

strand of nucleic acid

bool IsPacked_pnt(void) const

Check if variant Packed_pnt is selected.

const TWhole & GetWhole(void) const

Get the variant data.

void SetId(TId &value)

Assign a value to Id data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

bool IsGeneral(void) const

Check if variant General is selected.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

E_Choice Which(void) const

Which variant is currently selected.

void SetFrom(TFrom value)

Assign a value to From data member.

const Tdata & Get(void) const

Get the member data.

TVersion GetVersion(void) const

Get the Version member data.

void SetFuzz_to(TFuzz_to &value)

Assign a value to Fuzz_to data member.

void SetFuzz_from(TFuzz_from &value)

Assign a value to Fuzz_from data member.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

Tdata & Set(void)

Assign a value to data member.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsInt(void) const

Check if variant Int is selected.

bool IsSetVersion(void) const

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

void SetStrand(TStrand value)

Assign a value to Strand data member.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TAccession & GetAccession(void) const

Get the Accession member data.

@ eNa_strand_both

in forward orientation

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_Tpg

Third Party Annot/Seq Genbank.

const TSeq & GetSeq(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

@ eClass_segset

segmented sequence + parts

TRepr GetRepr(void) const

Get the Repr member data.

list< CRef< CSeqdesc > > Tdata

bool IsSetReplaced_by(void) const

these seqs make this one obsolete Check if a value has been assigned to Replaced_by data member.

const TUser & GetUser(void) const

Get the variant data.

bool CanGetType(void) const

Check if it is safe to call GetType method.

TLinkage GetLinkage(void) const

Get the Linkage member data.

const TInst & GetInst(void) const

Get the Inst member data.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

bool IsOrg(void) const

Check if variant Org is selected.

void SetExt(TExt &value)

Assign a value to Ext data member.

TType GetType(void) const

Get the Type member data.

bool CanGetLinkage_evidence(void) const

Check if it is safe to call GetLinkage_evidence method.

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

const TId & GetId(void) const

Get the Id member data.

bool IsSetHist(void) const

sequence history Check if a value has been assigned to Hist data member.

bool IsSetExt(void) const

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

const Tdata & Get(void) const

Get the member data.

bool IsSetInst(void) const

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

TLength GetLength(void) const

Get the Length member data.

const TOrg & GetOrg(void) const

Get the variant data.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

TMol GetMol(void) const

Get the Mol member data.

const TIds & GetIds(void) const

Get the Ids member data.

const TLinkage_evidence & GetLinkage_evidence(void) const

Get the Linkage_evidence member data.

TType GetType(void) const

Get the Type member data.

bool IsDelta(void) const

Check if variant Delta is selected.

void SetInst(TInst &value)

Assign a value to Inst data member.

const THist & GetHist(void) const

Get the Hist member data.

const TExt & GetExt(void) const

Get the Ext member data.

bool CanGetType(void) const

Check if it is safe to call GetType method.

ETopology

topology of molecule

const TDelta & GetDelta(void) const

Get the variant data.

bool CanGetLinkage(void) const

Check if it is safe to call GetLinkage method.

const Tdata & Get(void) const

Get the member data.

bool IsSetDate(void) const

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

list< CRef< CDelta_seq > > Tdata

bool IsGap(void) const

Check if variant Gap is selected.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

const TDate & GetDate(void) const

Get the Date member data.

const TReplaced_by & GetReplaced_by(void) const

Get the Replaced_by member data.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

list< CRef< CLinkage_evidence > > TLinkage_evidence

bool IsSetLinkage_evidence(void) const

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

bool IsUser(void) const

Check if variant User is selected.

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Org

if all from one organism

@ e_Molinfo

info on the molecule and techniques

@ e_Source

source of materials, includes Org-ref

@ eType_clone

Deprecated. Used only for AGP 1.1.

@ eType_fragment

Deprecated. Used only for AGP 1.1.

@ eType_proximity_ligation

@ e_Literal

a piece of sequence

@ e_Loc

point to a sequence

unsigned int

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

Definition of all error codes used in objmgr libraries (xobjmgr.lib, xobjutil.lib and others).

double value_type

The numeric datatype used by the parser.

const GenericPointer< typename T::ValueType > T2 value

Int4 delta(size_t dimension_, const Int4 *score_)

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

#define FOR_EACH_SEQDESC_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQDESC_ON_BIOSEQ EDIT_EACH_SEQDESC_ON_BIOSEQ.

#define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQID_ON_BIOSEQ EDIT_EACH_SEQID_ON_BIOSEQ.

void x_Translate(const Container &seq, string &prot, unsigned int frame, const CGenetic_code *code, bool is_5prime_complete, bool is_3prime_complete, bool include_stop, bool remove_trailing_X, bool *alt_start)

DEFINE_STATIC_ARRAY_MAP(TComplement, sc_Complement, sc_comp_tbl)

map< CCdregion::EFrame, SFrameInfo > TFrameInfoMap

int FastaNARank_SeqIdHandle(const CSeq_id_Handle &idh)

static void AddGapToDeltaSeq(CRef< CBioseq >prot, bool unknown_length, TSeqPos add_len)

CSeq_id_Handle x_FindLatestSequence(const CSeq_id_Handle &idh, CScope &scope, const CTime *tlim)

static const char sc_EnumToChar[16]

pair< Int8, CConstRef< CSeq_feat > > TFeatScore

int Score_SeqIdHandle(const CSeq_id_Handle &idh)

int FastaAARank_SeqIdHandle(const CSeq_id_Handle &idh)

static bool s_ShouldUseOriginalID(const CBioseq &seq)

int WorstRank_SeqIdHandle(const CSeq_id_Handle &idh)

static CConstRef< CSeq_feat > x_GetBestOverlapForSNP(const CSeq_feat &snp_feat, CSeqFeatData::E_Choice type, CSeqFeatData::ESubtype subtype, CScope &scope, bool search_both_strands=true)

static bool s_WriteGnlAndAcc(const CBioseq &bioseq, CNcbiOstream &ostr)

int BestRank_SeqIdHandle(const CSeq_id_Handle &idh)

static const TCharPair sc_comp_tbl[32]

bool IsTransSpliced(const CSeq_feat &feat)

static void AddAAToDeltaSeq(CRef< CBioseq > prot, char residue)

CSeq_id_Handle x_GetId(const CScope::TIds &ids, EGetIdType type)

CConstRef< CSeq_feat > GetLocalGeneByXref(const CGene_ref &gene, CBioseq_Handle bsh)

static string s_FastaGetOriginalID(const CBioseq &seq)

static char s_GetComplement(char c)

CConstRef< CSeq_feat > GetLocalGeneByLocus(const string &locus, bool use_tag, CBioseq_Handle bsh)

vector< TFeatScore > TFeatScores

const char * kRibosomalSlippageText

static string s_GetReverseComplement(const string &sequence)

CStaticPairArrayMap< Char, Char > TComplement

SStaticPair< Char, Char > TCharPair

static const EBaseCode sc_CharToEnum[256]

conversion table from Ncbi4na / Iupacna to EBaseCode

Generic utility macros and templates for exploring NCBI objects.

#define FIELD_IS_SET_AND_IS(Var, Fld, Chs)

FIELD_IS_SET_AND_IS base macro.

#define GET_FIELD(Var, Fld)

GET_FIELD base macro.

static CNamedPipeClient * client

This indicates the text of the modifiers of a gap.

bool operator()(const pair< T, U > &p1, const pair< T, U > &p2) const

bool operator()(const pair< T, U > &p1, const pair< T, U > &p2) const

Location relative to a base Seq-loc: one (usually) or more ranges of offsets.

Selector used in CSeqMap methods returning iterators.

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

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