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

tlabel = feat.GetData().GetKey();

(feat.GetData().IsImp()) {

( tlabel ==

) {

tlabel =

;

( tlabel !=

) {

tlabel =

+ tlabel +

;

&& feat.GetData().GetRegion() ==

&& feat.IsSetComment() ) {

}

(feat.GetData().IsImp()) {

tlabel =

+ feat.GetData().GetImp().GetKey() +

;

tlabel =

;

feat_it; ++feat_it) {

feat_it->GetData().GetProt().GetLabel(tlabel);

(

<<

+

.AsFastaString());

(

);

+=

;

+=

;

+=

;

+=

;

+=

;

+=

;

* type_label)

&& feat.

().find(*type_label) == string::npos) {

}

(type_label) {

*

+= *type_label;

* type_label)

(!

.IsSetExt()) {

(

.GetExt().Which()) {

tmp_label =

.GetExt().GetName();

(tmp_label ==

|| tmp_label ==

|| tmp_label ==

)) {

((*q)->GetQual() ==

) {

tmp_label = (*q)->GetVal();

((

&

) == 0 && type_label != 0 && !tmp_label.empty() && tmp_label.find(*type_label) == string::npos) {

*

+= *type_label +

+ tmp_label;

}

(!tmp_label.empty()) {

*

+= tmp_label;

}

(type_label) {

*

+= *type_label;

( !

.GetExt().GetTRNA().IsSetAa() ) {

.GetExt().GetTRNA().GetAa().Which();

(aa_code_type) {

aa_code =

.GetExt().GetTRNA().GetAa().GetIupacaa();

aa_code =

.GetExt().GetTRNA().GetAa().GetNcbieaa();

aa_code =

.GetExt().GetTRNA().GetAa().GetNcbi8aa();

aa_code =

.GetExt().GetTRNA().GetAa().GetNcbistdaa();

*

+= *type_label +

+ tmp_label;

}

(!tmp_label.empty()) {

*

+= tmp_label;

}

(type_label) {

*

+= *type_label;

(

.GetExt().GetGen().CanGetProduct()) {

*

=

.GetExt().GetGen().GetProduct();

}

(

.GetExt().GetGen().CanGetClass()) {

*

=

.GetExt().GetGen().GetClass();

( dbtag.

() ==

) {

( !tlabel->empty() ) {

*tlabel +=

.GetStr();

* type_label)

*tlabel += (*it)->GetVal();

*tlabel += type_label ? *type_label :

(

);

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

(pos == string::npos) {

*tlabel += feat.

().substr(0, pos);

*tlabel += type_label ? *type_label :

(

);

std_name, func, num, other;

(other.empty()) other = (*it)->GetVal();

(std_name.empty() &&

((*it)->GetQual(),

)) {

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

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

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

(!std_name.empty()) {

(!other.empty()) {

*tlabel += type_label ? *type_label :

(

);

( !tlabel->empty() ) {

* type_label,

tlabel += CSeqFeatData::GetTypeInfo_enum_EBond()

tlabel += CSeqFeatData::GetTypeInfo_enum_ESite()

tlabel += CSeqFeatData::GetTypeInfo_enum_EPsec_str()

( !

.empty() ) {

(*iter)->GetLabel(&

);

(!tlabel.empty()) {

prefix(

);

tlabel += prefix + (**it).GetQual();

(!(**it).GetVal().empty()) {

tlabel +=

+ (**it).GetVal();

(tlabel.empty()) {

*

+= type_label;

label_len =

->size();

*

+= type_label;

(label_type) {

mapped =

;

(

.IsLocal() ) {

(

.IsId() ) {

old_id =

.GetId();

new_id =

(old_id, tse);

( new_id != old_id ) {

.SetId(new_id);

mapped =

;

(

.IsLocal() ) {

(

.IsId() ) {

old_id =

.GetId();

( new_id != old_id ) {

.SetId(new_id);

mapped =

;

( oid1.

() ) {

oid1int = oid1.

();

oid2int = oid2.

();

( oid1int != oid2int ) {

oid1int < oid2int;

( oid1.

() ) {

& oid1str = oid1.

();

& oid2str = oid2.

();

(

it(master_seq, range, sel); it; ++it ) {

( it->GetSeq_feat_Handle() == feat ) {

);

( !master_seq ) {

);

( !master_seq ) {

);

: m_StartType(start ==

::eSubtype_bad? subtype: start),

m_CurrentType(subtype),

m_ByProduct(

)

( subtype ) {

sm_SpecialVDJTypes;

sx_IsIrregularLocation(

& loc,

( !loc.

() ) {

( !loc.

() ) {

plus_strand = !

(strand);

( sx_IsIrregularLocation(loc1, circular_length) ) {

( range.

() ) {

( plus_strand ) {

( range.

() < pos ) {

pos = range.

()+1;

( range.

() > pos ) {

* single_id = 0;

kQual_transcript_id[] =

;

kQual_orig_transcript_id[] =

;

kQual_orig_protein_id[] =

;

kQualPriority_transcript_id,

kQualPriority_orig_transcript_id,

kQualPriority_orig_protein_id,

SMatchingQuals {

( (*it)->IsSetVal() ) {

& qual = (*it)->GetQual();

( qual == kQual_orig_protein_id ||

qual == kQual_orig_transcript_id ||

qual == kQual_transcript_id ) {

SMatchingQuals(

& feat)

( (*it)->IsSetVal() ) {

& qual = (*it)->GetQual();

( qual == kQual_orig_protein_id ) {

qq[kQualPriority_orig_protein_id] = *it;

( qual == kQual_orig_transcript_id ) {

qq[kQualPriority_orig_transcript_id] = *it;

( qual == kQual_transcript_id ) {

qq[kQualPriority_transcript_id] = *it;

GetMatch(

SMatchingQuals& quals2)

(

= 0;

< kQualPriority_count; ++

) {

( qq[

] && quals2.qq[

] &&

qq[

]->GetVal() == quals2.qq[

]->GetVal() ) {

SMatchingQuals::HasMatch(feat);

( xrefs.size() == 1 ) {

(

.IsGene() ) {

SMatchingQuals quals1(feat1);

SMatchingQuals quals2(feat2);

quals1.GetMatch(quals2);

(

|| sx_IsIrregularLocation(loc, circular_length)) ) {

overlap_type;

( feat_type != parent_type ) {

(

link(feat_type); link; ++link ) {

kBetterTypeParentQuality= 1000;

kByLocusParentQuality = 750;

kSameTypeParentQuality = 500;

kWorseTypeParentQuality = kSameTypeParentQuality;

d_child = sx_GetRootDistance(child);

d_parent = sx_GetRootDistance(parent);

( d_parent < d_child ) {

kBetterTypeParentQuality - (d_child - d_parent);

kWorseTypeParentQuality - (d_parent - d_child);

(

.IsLocal() ) {

(

.IsGene() ) {

sx_GetOverlapType(link, c_loc, circular_length);

sel.IncludeFeatSubtype(*type_ptr);

( overlap >= 0 && overlap < best_overlap ) {

best_overlap = overlap;

best_parent = sx_GetParentByRef(feat, link);

( best_parent ) {

best_parent = sx_GetParentByOverlap(feat, link, circular_length);

( best_parent ) {

CheckBest(

quality,

overlap, CFeatInfo*

)

( (quality > m_Quality ||

(quality == m_Quality && overlap < m_Overlap)) ) {

m_Quality = quality;

m_Overlap = overlap;

CheckBest(

SBestInfo&

)

CheckBest(

.m_Quality,

.m_Overlap,

.m_Info);

SFeatRangeInfo {

x_CanonizeId(TCanonicalIdsMap& ids_map)

iter = ids_map.find(m_Id);

( iter != ids_map.end() ) {

m_Id = iter->second;

m_Info->m_Feat.GetScope(),

ids_map[m_Id] = new_id;

SFeatRangeInfo(TCanonicalIdsMap& ids_map,

CFeatInfo&

, SBestInfo* best,

by_product =

)

m_SplitRange(

),

m_Id =

.m_Feat.GetProductId();

m_Range =

.m_Feat.GetProductTotalRange();

m_Id =

.m_Feat.GetLocationId();

m_Range =

.m_Feat.GetLocationTotalRange();

x_CanonizeId(ids_map);

SFeatRangeInfo(TCanonicalIdsMap& ids_map,

CFeatInfo&

, SBestInfo* best,

: m_Id(it->

),

m_Range(it->second.GetOverlappingRange()),

m_SplitRange(

),

x_CanonizeId(ids_map);

PLessByStart {

operator()(

SFeatRangeInfo&

,

SFeatRangeInfo&

)

.m_Id <

.m_Id ||

(

.m_Id ==

.m_Id &&

.m_Range <

.m_Range);

operator()(

SFeatRangeInfo&

,

SFeatRangeInfo&

)

.m_Id <

.m_Id ||

(

.m_Id ==

.m_Id &&

(

.m_Range.GetToOpen() <

.m_Range.GetToOpen() ||

(

.m_Range.GetToOpen() ==

.m_Range.GetToOpen() &&

.m_Range.GetFrom() <

.m_Range.GetFrom())));

s_AddCircularRanges(vector<SFeatRangeInfo>& rr,

SFeatRangeInfo& range_info,

by_product =

)

kAllowOriginInGap =

;

( !kAllowOriginInGap && range_info.m_Range.GetFrom() != 0 ) {

range_info.m_Info->m_Feat.GetProduct():

range_info.m_Info->m_Feat.GetLocation();

( start <= stop ) {

circular_length = sx_GetCircularLength(range_info.m_Info->m_Feat.GetScope(), range_info.m_Id);

( !kAllowOriginInGap && range_info.m_Range.GetToOpen() < circular_length ) {

total_end_open = range_info.m_Range.GetToOpen();

range_info.m_SplitRange =

;

range_info.m_Range.SetTo(stop);

rr.push_back(range_info);

range_info.m_Range.SetFrom(start);

range_info.m_Range.SetToOpen(total_end_open);

rr.push_back(range_info);

s_AddRanges(TCanonicalIdsMap& ids_map,

vector<SFeatRangeInfo>& rr,

.m_MultiId =

;

SFeatRangeInfo range_info(ids_map,

, best, it);

rr.push_back(range_info);

vector<SBestInfo> TBestArray;

vector<SFeatRangeInfo> TRangeArray;

vector<CFeatTree::CFeatInfo*> TInfoArray;

sx_GetQualMatch(feat.

, parent.

);

CFeatTreeParentTypeIndex :

m_ByProduct(by_product),

TRangeArray& GetIndex(TCanonicalIdsMap& ids_map,

TInfoArray& feats) {

( m_IndexedParents == feats.size() ) {

(

ind = m_IndexedParents; ind < feats.size(); ++ind ) {

( feat_info.

< m_IndexedParents ||

SFeatRangeInfo range_info(ids_map, feat_info, 0, m_ByProduct);

( range_info.m_Id ) {

( !s_AddCircularRanges(m_Index, range_info, m_ByProduct) ) {

m_Index.push_back(range_info);

s_AddRanges(ids_map,

m_Index, feat_info, 0,

(m_Index.begin(), m_Index.end(), PLessByEnd());

m_IndexedParents = feats.size();

m_IndexedParents;

TRangeArray m_Index;

TInfoArray& feats) {

index =

CFeatTreeParentTypeIndex(

, by_product);

(

!= &ft ) {

( ; it; ++it ) {

);

( !

.m_Feat ) {

.m_AddIndex = index;

.m_Feat = feat;

.m_CanMatchByQual = sx_CanMatchByQual(feat);

.m_IsSetGene = sx_GeneSuppressed(feat);

);

);

it->second.m_Feat;

pair<int, CFeatTree::CFeatInfo*>

pair<int, CFeatInfo*> ret(0,

);

( !

.m_Feat.IsSetXref() ) {

( !

.IsLocal() ) {

vector<CSeq_feat_Handle> ff =

( vector<CSeq_feat_Handle>, fit, ff ) {

sx_GetParentTypeQuality(parent->

(),

.GetSubtype());

( quality > ret.first ) {

ret.first = quality;

ret.second = parent;

( ret.first > kByLocusParentQuality ) {

.GetSubtype()) ) {

(

.IsGene() ) {

vector<CSeq_feat_Handle> ff =

( vector<CSeq_feat_Handle>, fit, ff ) {

ret.first = kByLocusParentQuality;

ret.first = kByLocusParentQuality;

pair<int, CFeatInfo*> parent =

( !parent.second ) {

( parent.first <= kWorseTypeParentQuality ||

parent.first == kSameTypeParentQuality ) {

( parent.second->IsSetParent() &&

parent.second->m_Parent == &

) {

pair<int, CFeatInfo*> grand_parent =

( grand_parent.second == &

) {

( parent.first < grand_parent.first ) {

( parent.second->IsGene() ) {

( !

.IsSetGene() ) {

->GetSNPStrandMode() ==

->eSNPStrand_both ) {

(

.m_Feat.IsSetExcept_text() &&

.m_Feat.GetExcept_text().find(

) !=

) {

(

SBestInfo& info1,

SBestInfo& info2)

{

(info1.m_Info && info2.m_Info) {

(info1.m_Quality != info2.m_Quality) {

info1.m_Quality > info2.m_Quality;

(info1.m_Overlap != info2.m_Overlap) {

info1.m_Overlap < info2.m_Overlap;

info1.m_Info < info2.m_Info;

= features.size();

(

= 0;

<

; ++

) {

( c->GetSubtype() == subtype ) {

.CheckBest(quality, overlap, parent);

(cr1.first == cr2.first)

;

(cr1.second.parents.size() != cr2.second.parents.size()) {

cr1.second.parents.size() < cr2.second.parents.size();

(!cr1.second.parents.empty()) {

SBestInfo& p1 = *cr1.second.parents.begin();

SBestInfo& p2 = *cr2.second.parents.begin();

(p1.m_Quality != p2.m_Quality)

p1.m_Quality > p2.m_Quality;

(p1.m_Overlap != p2.m_Overlap)

p1.m_Overlap < p2.m_Overlap;

(

!= 0)

< 0;

(

!= 0)

< 0;

( !f2.

() )

;

(

!= 0)

< 0;

( !giim2.

() )

;

(

!= 0)

< 0;

( giim2.

() )

;

(

!= 0)

< 0;

( oid1.

() ) {

( !oid2.

() )

;

( oid1.

() ) {

( !oid2.

() )

;

(

!= 0)

< 0;

( f2.

() )

;

TOrderedChildren ordered_children;

(ci->second.parents.empty())

;

ordered_children.insert(ci);

(TOrderedChildren, ci, ordered_children) {

(child.second.parents.empty())

;

bests[(*ci)->second.index] = *child.second.parents.begin();

* parent = child.second.parents.begin()->m_Info;

(bi->m_Info == parent) {

(*pci == (*ci)->first)

;

(

.m_Info == parent) {

.m_Info =

;

.GetFrom() <

.GetFrom() ||

.GetToOpen() >

.GetToOpen();

TCanonicalIdsMap& ids_map)

check_genes =

;

(

->GetGeneCheckMode() ==

->eGeneCheck_match &&

->GetBestGene(features[0]->m_Feat,

->eBestGene_OverlappedOnly);

check_genes =

;

= features.size();

bests.resize(

);

(

= 0;

<

; ++

) {

SBestInfo* best = &bests[

];

SFeatRangeInfo range_info(ids_map, feat_info, best);

( range_info.m_Id ) {

( !s_AddCircularRanges(cc, range_info) ) {

cc.push_back(range_info);

(cc.begin(), cc.end(), PLessByStart());

pair<CFeatTree::CFeatInfo*, CFeatTree::CFeatInfo*> TFeatPair;

TRangeArray::iterator

= pp.begin();

TRangeArray::iterator ci = cc.begin();

( ; ci != cc.end(); ) {

(

!= pp.end() &&

->m_Id < ci->m_Id ) {

(

== pp.end() ) {

( ci->m_Id < cur_id || !ci->m_Id ) {

}

( ci != cc.end() && (ci->m_Id < cur_id || !ci->m_Id) );

TRangeArray::iterator pe =

;

( pe != pp.end() && pe->m_Id == cur_id ) {

sx_GetCircularLength(

->m_Info->m_Feat.GetScope(), cur_id);

TRangeArray::iterator

= pe;

->m_MinFrom = min_from;

min_from =

(min_from, (--

)->m_Range.

());

->m_MinFrom = min_from;

( ; ci != cc.end() &&

!= pe && ci->m_Id == cur_id; ++ci ) {

sx_GetOverlapType(link, c_loc, circular_length);

->m_Range.GetToOpen() < ci->m_Range.GetFrom() ) {

( TRangeArray::iterator pc =

;

pc != pe && pc->m_MinFrom < ci->m_Range.GetToOpen();

( !pc->m_Range.IntersectingWith(ci->m_Range) ) {

( check_genes &&

.IsSetGene() ) {

(

.m_Gene != pc->m_Info->GetChildrenGene() ) {

(

.m_MultiId && pc->m_Info->m_MultiId &&

!multi_id_tested.

(TFeatPair(&

, pc->m_Info)).second ) {

quality = s_GetParentQuality(

, *pc->m_Info);

ci->m_Id && pc->m_Id &&

( overlap >= 0 ) {

( !disambibuator.

(ci->m_Info, pc->m_Info, quality, overlap) ) {

ci->m_Best->CheckBest(quality, overlap, pc->m_Info);

(

.m_MultiId || pc->m_Info->m_MultiId ) {

( !c_loc2 || c_loc2_strand != pstrand ) {

c_loc2_strand = pstrand;

( overlap >= 0 ) {

disambibuator.

(ci->m_Info, pc->m_Info, quality, overlap);

ci->m_Best->CheckBest((

)(quality-1), overlap, pc->m_Info);

( ; ci != cc.end() && ci->m_Id == cur_id; ++ci ) {

( features.empty() ) {

unassigned =

;

( !

.IsSetParent() ) {

(

.IsSetGene() ) {

(

.m_Gene ) {

( !unassigned ) {

( parents.empty() ) {

( bests.empty() ) {

(bests, bests1);

(

= 0;

< bests1.size(); ++

) {

bests[

].CheckBest(bests1[

]);

( bests.empty() ) {

( parents.empty() ) {

= features.size();

TFeatArray::iterator dst = features.begin();

(

= 0;

<

; ++

) {

( !

.IsSetParent() ) {

features.erase(dst, features.end());

( features.empty() ) {

TRangeArray& genes =

( genes.empty() ) {

= features.size();

(

= 0;

<

; ++

) {

( !

.IsSetGene() ) {

(

.IsSetGene() ) {

has_genes =

;

( !

.IsSetGene() &&

(feat_type).CanHaveGeneParent() ) {

( !old_feats.empty() ) {

old_feats.insert(old_feats.end(),

new_feats.begin(), new_feats.end());

(old_feats, new_feats);

( has_genes && !new_feats.empty() ) {

vector<TFeatArray> feats_by_type;

new_count = 0;

(

.IsSetParent() ) {

index = feat_type;

( index >= feats_by_type.size() ) {

feats_by_type.resize(index+1);

feats_by_type[feat_type].push_back(&

);

( new_count == 0 ) {

(

= 0;

< feats_by_type.size(); ++

) {

( feats.empty() ) {

( feats.empty() ) {

(

.m_IsLinkedToRoot ==

.eIsLinkedToRoot_linking ) {

<<

.m_Feat.GetOriginalFeature()

<<

.m_Parent->m_Feat.GetOriginalFeature()

);

(

.m_Parent ) {

.m_IsLinkedToRoot =

.eIsLinkedToRoot_linking;

.m_IsLinkedToRoot =

.eIsLinkedToRoot_linked;

.m_Parent = &parent;

.m_IsSetParent =

;

.m_IsSetParent =

;

.m_IsLinkedToRoot =

.eIsLinkedToRoot_linked;

.m_Gene = gene;

.m_IsSetGene =

;

( !

.IsSetParent() ) {

.m_Parent;

.m_Children;

ret =

->m_Feat;

vector<CMappedFeat> children;

vector<CMappedFeat>& children)

children.reserve(infos->size());

children.push_back((*it)->m_Feat);

m_CanMatchByQual(

),

m_IsSetParent(

),

m_IsSetGene(

),

m_IsSetChildren(

),

m_IsLinkedToRoot(eIsLinkedToRoot_unknown),

m_Feat.GetAnnot().GetTSE_Handle();

( skip_bottom ) {

( top_type != bottom_type ) {

(

link(bottom_type); link; ++link ) {

bottom_type, top_type, base_sel);

);

.AddGenesForMrna(mrna_feat, base_sel);

.GetBestGene(mrna_feat, lookup_type);

feat_tree->

(mrna_feat, lookup_type);

);

.AddGenesForCds(cds_feat, base_sel);

.GetBestGene(cds_feat, lookup_type);

feat_tree->

(cds_feat, lookup_type);

);

.AddMrnasForCds(cds_feat, base_sel);

);

.AddCdsForMrna(mrna_feat, base_sel);

vector<CMappedFeat>& children = feat_tree->

(mrna_feat);

( vector<CMappedFeat>, it, children ) {

list< CMappedFeat >& mrna_feats,

);

.AddMrnasForGene(gene_feat, base_sel);

vector<CMappedFeat>& children = feat_tree->

(gene_feat);

( vector<CMappedFeat>, it, children ) {

mrna_feats.push_back(*it);

list< CMappedFeat >& cds_feats,

);

.AddCdsForGene(gene_feat, base_sel);

vector<CMappedFeat>& children = feat_tree->

(gene_feat);

( vector<CMappedFeat>, it, children ) {

vector<CMappedFeat>& children2 = feat_tree->

(*it);

( vector<CMappedFeat>, it2, children2 ) {

cds_feats.push_back(*it2);

cds_feats.push_back(*it);

);

.AddGenesForFeat(feat, base_sel);

.GetBestGene(feat, lookup_type);

feat_tree->

(feat, lookup_type);

);

.AddFeaturesFor(feat, parent_type, base_sel);

.GetParent(feat, parent_type);

feat_tree->

(feat, parent_type);

revert_locations =

;

(overlap_type) {

revert_locations =

;

( loc.

() ) {

* single_id = 0;

(

<< e.GetMsg());

feat_it(h, range, strand, sel);

( ; feat_it; ++feat_it) {

cur_diff = ( !revert_locations ) ?

feats.push_back(sc);

( ; feat_it; ++feat_it) {

cur_diff = ( !revert_locations ) ?

feats.push_back(sc);

(

);

overlap_type, scores, base_sel);

( !scores.empty() ) {

max_element(scores.begin(), scores.end())->second;

min_element(scores.begin(), scores.end())->second;

( need_subtype ) {

need_subtype, overlap_type, 0, base_sel);

severe_feat_exception =

(severe_feat_exception ||

(

feat_it(annot); feat_it; ++feat_it ) {

(

feat_it(entry); feat_it; ++feat_it ) {

vector<CMappedFeat> children = ft.

(parent);

(vector<CMappedFeat>, it, children ) {

stop->

().SetId().Assign(citer.GetSeq_id());

pos1_not_in =

;

(pos1 == ((

)-1)) {

pos1_not_in =

;

pos2_not_in =

;

(pos2 == ((

)-1)) {

pos2_not_in =

;

(pos1_not_in && pos2_not_in) {

frame = 0;

mod1 = (pos1 + 3 - frame) %3;

}

(pos1 < frame) {

mod2 = (pos2 + 3 - frame) %3;

&& pos2 == cds_len) {

}

(pos2 <= frame) {

(pos2 > cds_len) {

( (mod1 != 0) && (mod2 != 2) ) {

}

(mod1 != 0) {

}

(mod2 != 2) {

(!orig_feat.IsSetData() || !orig_feat.GetData().IsCdregion()) {

(orig_feat.IsSetPseudo() && orig_feat.GetPseudo()) {

(parent_entry.

()

(; annot_ci; ++annot_ci) {

((*annot_ci).IsFtable()) {

new_annot->

().SetFtable();

orig_feat = new_annot.

(feh);

(feat_list.empty())

any_change =

;

should_be_partial = partial5 || partial3;

is_partial =

;

(should_be_partial && !is_partial) {

(!should_be_partial && is_partial) {

any_change =

;

((partial5 && !prot_5) || (!partial5 && prot_5)

|| (partial3 && !prot_3) || (!partial3 && prot_3)) {

(partial5 && partial3) {

(partial5) {

(partial3) {

any_change =

;

new_feat->

(*(

->GetSeq_feat()));

found =

;

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

beh.

().Set().push_back(new_molinfo_desc);

(!prot_bsh || !prot_bsh.

())

(new_protein && new_protein->

()) {

new_feat->

(*(

->GetSeq_feat()));

added =

;

((*it)->IsFtable()) {

annot->

().SetFtable().push_back(sf);

new_prot->

().SetProt().SetName().push_back(protein_name);

vector<CMappedFeat>& children,

feature::CFeatTree& featTree)

vector<CMappedFeat> c = featTree.GetChildren(mf);

(vector<CMappedFeat>::iterator it = c.begin(); it != c.end(); it++) {

(

.GetFeatSubtype() == subtype) {

children.push_back(

);

vector<CMappedFeat>& children)

feature::CFeatTree myTree;

vector<CMappedFeat> c = myTree.GetChildren(mf);

(vector<CMappedFeat>::iterator it = c.begin(); it != c.end(); it++) {

(

.GetFeatSubtype() == subtype) {

children.push_back(

);

feature::CFeatTree& ft,

vector<CMappedFeat> MFS;

MFS::const_iterator MFSit;

strRearrange(

);

vector<CMappedFeat> vecCds;

(MFSit it = vecCds.begin(); it != vecCds.end(); it++) {

(it->IsSetPseudo() && it->GetPseudo()) {

(it->IsSetExcept_text() && (it->GetExcept_text() == strRearrange)) {

biotype =

;

vector<CMappedFeat> vecOthers;

(MFSit it = vecOthers.begin(); it != vecOthers.end(); it++) {

(!geneIsPseudo && (!it->IsSetPseudo() || !it->GetPseudo())) {

(singleSubtype ==

(bad)) {

singleSubtype = currentSubtype;

(currentSubtype != singleSubtype) {

singleSubtype =

(bad);

vector<string> acceptedClasses = {

,

,

(singleSubtype ==

(ncRNA) && nonPseudo) {

(!

.IsSetExt()) {

(!ext.

()) {

(rnaClass ==

) {

(std::find(acceptedClasses.begin(), acceptedClasses.end(), rnaClass) ==

acceptedClasses.end()) {

(singleSubtype !=

(bad) && nonPseudo) {

(singleSubtype ==

(otherRNA)) {

biotype =

;

(singleSubtype !=

(bad)) {

(MFSit it = vecCds.begin(); it != vecCds.end(); it++) {

(!it->IsSetExcept_text()) {

(it->GetExcept_text() != strRearrange) {

(it->IsSetPseudo() && it->GetPseudo()) {

biotype =

;

biotype =

;

biotype =

;

feature::CFeatTree& ft,

feature::CFeatTree& ft,

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.

bool IsReverse(ENa_strand s)

@ eExtreme_Biological

5' and 3'

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.

@ eBoth

Both preliminary and traceback stages.

CSeq_annot_Handle GetAnnot(void) const

TSeqPos GetLength(void) const

int Compare(const CDbtag &dbt2) const

set< SBestInfo, SBestInfoLess > TBestSet

void Disambiguate(TBestArray &bests)

CFeatTree::CFeatInfo CFeatInfo

map< CFeatInfo *, SCandidates > TChildren

bool Add(CFeatInfo *child, CFeatInfo *parent, Int1 quality, Int8 overlap)

list< CFeatInfo * > TChildList

map< CFeatInfo *, SParentInfo > TParents

CDisambiguator(CFeatTree::TFeatArray &features)

map< TParentKey, CRef< CFeatTreeParentTypeIndex > > TIndex

TRangeArray & GetIndex(CSeqFeatData::ESubtype type, bool by_product, const TInfoArray &feats)

pair< CSeqFeatData::ESubtype, bool > TParentKey

TRangeArray & GetIndex(const STypeLink &link, const TInfoArray &feats)

TCanonicalIdsMap m_CanonicalIds

void GetLabel(string *label) const

void AddLocation(const CSeq_loc &loc, ETransSplicing trans_splcing=eNoTransSplicing)

TLocMap::const_iterator const_iterator

Base class for all object manager exceptions.

Exceptions for objmgr/util library.

void GetLabel(string *label) const

void GetLabel(string *label) const

bool GetLabel(string *label, TLabelFlags flags=0, ELabelVersion version=eLabel_DefaultVersion) const override

Append a label to "label" based on content.

bool GetLabel(string *label, TLabelFlags flags=0, ELabelVersion version=eLabel_DefaultVersion) const override

Get a label that is the concatenation of the pub labels for the pubs in the set.

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

ESubtype GetSubtype(void) const

static E_Choice GetTypeFromSubtype(ESubtype subtype)

@ eSubtype_transit_peptide

@ eSubtype_misc_structure

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

@ eSubtype_mobile_element

static CTempString SubtypeValueToName(ESubtype eSubtype)

Turns a ESubtype into its string value which is NOT necessarily related to the identifier of the enum...

CSeq_feat_EditHandle –.

namespace ncbi::objects::

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 const string & GetCode(CSeq_data::E_Choice code_type, TIndex idx)

static const string & GetIupacaa3(TIndex ncbistdaa)

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

CSeq_feat_Handle GetGeneByRef(const CGene_ref &ref) const

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

TSeq_feat_Handles GetGenesByRef(const CGene_ref &ref) const

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator end() const

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static unsigned char depth[2 *(256+1+29)+1]

static vector< string > arr

static void s_GetRnaRefLabelFromComment(const CSeq_feat &feat, string *label, TFeatLabelFlags flags, const string *type_label)

static CMappedFeat GetBestOverlappingFeat(CScope &scope, const CSeq_loc &loc, CSeqFeatData::ESubtype feat_subtype, sequence::EOverlapType overlap_type, TBestFeatOpts opts, const SAnnotSelector *base_sel)

bool sFeatureGetChildrenOfSubtypeFaster(CMappedFeat, CSeqFeatData::ESubtype, vector< CMappedFeat > &, feature::CFeatTree &)

bool sGetFeatureGeneBiotypeWrapper(feature::CFeatTree &, CMappedFeat, string &, bool)

pair< Int8, CMappedFeat > TMappedFeatScore

static const bool kOptimizeTestOverlap

void s_GetContentLabel(const CSeq_feat &feat, string *label, const string *type_label, TFeatLabelFlags flags, CScope *scope)

static void s_GetVariationLabel(const CSeq_feat &feat, string *tlabel, TFeatLabelFlags flags, const string *)

static EStrandMatchRule s_GetStrandMatchRule(const STypeLink &link, const CFeatTree::CFeatInfo &info, const CFeatTree *tree)

static const bool kSplitCircular

static void GetOverlappingFeatures(CScope &scope, const CSeq_loc &loc, CSeqFeatData::E_Choice, CSeqFeatData::ESubtype feat_subtype, sequence::EOverlapType overlap_type, TMappedFeatScores &feats, const SAnnotSelector *base_sel)

static void s_SetChildrenFeatureIds(CFeatTree &ft, const CMappedFeat &feat, int &feat_id)

void s_GetTypeLabel(const CSeq_feat &feat, string *label, TFeatLabelFlags flags)

static void s_GetVariationDbtagLabel(string *tlabel, TFeatLabelFlags, const CDbtag &dbtag)

static bool s_IsNotSubrange(const CRange< TSeqPos > &r1, const CRange< TSeqPos > &r2)

static void s_GetRnaRefLabel(const CSeq_feat &feat, string *label, TFeatLabelFlags flags, const string *type_label)

static bool s_AllowedParentByOverlap(CSeqFeatData::ESubtype child, CSeqFeatData::ESubtype parent)

static bool s_GetImpLabel(const CSeq_feat &feat, string *tlabel, TFeatLabelFlags flags, const string *type_label)

static void s_GetCdregionLabel(const CSeq_feat &feat, string *tlabel, CScope *scope)

vector< TMappedFeatScore > TMappedFeatScores

static void s_CollectBestOverlaps(CFeatTree::TFeatArray &features, TBestArray &bests, const STypeLink &link, TRangeArray &pp, CFeatTree *tree, TCanonicalIdsMap &ids_map)

static void s_SetFeatureId(CFeatTree &ft, const CMappedFeat &feat, int &last_id, const CMappedFeat &parent)

static CRef< CSeq_loc > s_MakePointForLocationStop(const CSeq_loc &loc)

@ eStrandMatch_at_least_one

bool sFeatureGetChildrenOfSubtype(CMappedFeat, CSeqFeatData::ESubtype, vector< CMappedFeat > &)

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

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERASE_ITERATE(Type, Var, Cont)

Non-constant version with ability to erase current element, if container permits.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

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)

#define ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

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 –.

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.

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

int Compare(const CSeq_loc &loc) const

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 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 SetStrand(ENa_strand strand)

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

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

void GetMrnasForGene(const CMappedFeat &gene_feat, list< CMappedFeat > &mrna_feats, CFeatTree *feat_tree, const SAnnotSelector *base_sel)

EGeneCheckMode m_GeneCheckMode

bool PromoteCDSToNucProtSet(objects::CSeq_feat_Handle &orig_feat)

Promotes coding region from Seq-annot on nucleotide sequence to Seq-annot on nuc-prot-set if necessar...

CFeatInfo & x_GetInfo(const CSeq_feat_Handle &feat)

CMappedFeat GetBestParentForFeat(const CMappedFeat &feat, CSeqFeatData::ESubtype parent_type, CFeatTree *feat_tree, const SAnnotSelector *base_sel)

bool m_IgnoreMissingGeneXref

CRef< CFeatTreeIndex > m_Index

void GetCdssForGene(const CMappedFeat &gene_feat, list< CMappedFeat > &cds_feats, CFeatTree *feat_tree, const SAnnotSelector *base_sel)

vector< CMappedFeat > GetChildren(const CMappedFeat &feat)

Return all nearest children of a feature.

bool x_AssignParentByRef(CFeatInfo &info)

CMappedFeat GetBestGeneForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree, const SAnnotSelector *base_sel, CFeatTree::EBestGeneType lookup_type)

void SetFeatIdMode(EFeatIdMode mode)

const CTSE_Handle & GetTSE(void) const

bool GetFeatureGeneBiotype(feature::CFeatTree &ft, CMappedFeat mf, string &biotype)

void GetLabel(const CSeq_feat &feat, string *label, TFeatLabelFlags flags, CScope *scope)

void SetSNPStrandMode(ESNPStrandMode mode)

void AddGenesForCds(const CMappedFeat &cds_feat, const SAnnotSelector *base_sel=0)

Add all necessary features to get genes for a cdregion feature.

void AddCdsForMrna(const CMappedFeat &mrna_feat, const SAnnotSelector *base_sel=0)

Add all necessary features to get cdregions for a mRNA feature.

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

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

void SetIgnoreMissingGeneXref(bool ignore=true)

CFeatInfo * GetChildrenGene(void)

void x_AssignParents(void)

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

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

CMappedFeat GetBestMrnaForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree, const SAnnotSelector *base_sel)

void x_SetGene(CFeatInfo &info, CFeatInfo *gene)

pair< int, CTSE_Handle > TFullId

vector< CFeatInfo * > TChildren

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

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

ESNPStrandMode

Mode of processing SNP strands.

void AddCdsForGene(const CMappedFeat &gene_feat, const SAnnotSelector *base_sel=0)

Add all necessary features to get cdregions for a gene feature.

const TChildren & x_GetChildren(CFeatInfo &info)

const CMappedFeat & GetMappedFeat(const CSeq_feat_Handle &feat) const

Find a corresponding CMappedFeat for a feature already added to a tree.

CMappedFeat GetBestGene(const CMappedFeat &feat, EBestGeneType lookup_type=eBestGene_TreeOnly)

Return parent gene if exists or best overlapping gene.

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree, const SAnnotSelector *base_sel, CFeatTree::EBestGeneType lookup_type)

void AddMrnasForGene(const CMappedFeat &gene_feat, const SAnnotSelector *base_sel=0)

Add all necessary features to get mRNAs for a gene feature.

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

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

void ClearFeatureIds(const CSeq_annot_EditHandle &annot)

void AddFeatureToBioseq(const CBioseq &seq, const CSeq_feat &f, CScope &scope)

AddFeatureToBioseq A function to add a feature to a Bioseq - will create a new feature table Seq-anno...

ELabelType

For compatibility with legacy code.

EBestGeneFeatIdMode m_BestGeneFeatIdMode

void x_AssignParentsByOverlap(TFeatArray &features, const STypeLink &link)

ESNPStrandMode m_SNPStrandMode

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

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

CMappedFeat GetBestGeneForFeat(const CMappedFeat &feat, CFeatTree *feat_tree, const SAnnotSelector *base_sel, CFeatTree::EBestGeneType lookup_type)

CMappedFeat GetParent(const CMappedFeat &feat)

Return nearest parent of a feature.

vector< CFeatInfo * > TFeatArray

EIsLinkedToRoot m_IsLinkedToRoot

void AddFeaturesFor(CScope &scope, const CSeq_loc &loc, CSeqFeatData::ESubtype bottom_type, CSeqFeatData::ESubtype top_type, const SAnnotSelector *base_sel=0, bool skip_bottom=false)

Add all features from bottom_type to top_type for a feature.

CRef< CSeq_loc_Mapper > CreateSeqLocMapperFromFeat(const CSeq_feat &feat, CSeq_loc_Mapper::EFeatMapDirection dir, CScope *scope)

Create CSeq_loc_Mapper from a feature, check for special cases like exceptions in CDS features.

void AddFeature(const CMappedFeat &feat)

Add a single feature to the tree.

bool GetIgnoreMissingGeneXref(void) const

Mode for taking into account gene xref to a missing genes.

bool AdjustFeaturePartialFlagForLocation(CSeq_feat &new_feat)

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

bool GetFeatureGeneBiotypeFaster(feature::CFeatTree &ft, CMappedFeat mf, string &biotype)

CMappedFeat MapSeq_feat(const CSeq_feat_Handle &feat, const CBioseq_Handle &master_seq, const CRange< TSeqPos > &range)

void SetGeneCheckMode(EGeneCheckMode mode)

void x_AssignGenesByOverlap(TFeatArray &features)

void GetChildrenTo(const CMappedFeat &feat, vector< CMappedFeat > &children)

Store all nearest children of a feature into a vector.

vector< CFeatInfo * > TChildren

void x_SetGeneRecursive(CFeatInfo &info, CFeatInfo *gene)

CMappedFeat GetParentFeature(const CMappedFeat &feat)

void x_SetNoParent(CFeatInfo &info)

pair< int, CFeatInfo * > x_LookupParentByRef(CFeatInfo &info, CSeqFeatData::ESubtype parent_type)

EGeneCheckMode

Mode for taking into account best gene eGeneCheck_match will try to match a parent feature only if th...

bool IsSetGene(void) const

size_t GetFeatIdsCount(void) const

~CFeatTree(void)

Destructor.

CSeqFeatData::ESubtype GetSubtype(void) const

virtual bool Less(const CSeq_feat &f1, const CSeq_feat &f2, CScope *scope)

void AddGenesForFeat(const CMappedFeat &feat, const SAnnotSelector *base_sel=0)

Add all necessary features to get genes for an arbitrary feature.

void x_VerifyLinkedToRoot(CFeatInfo &info)

vector< CFeatInfo * > TInfoArray

CFeatInfo * x_GetParent(CFeatInfo &info)

CFeatTree & operator=(const CFeatTree &)

int RemapId(int old_id, const CTSE_Handle &tse)

void AddMrnasForCds(const CMappedFeat &cds_feat, const SAnnotSelector *base_sel=0)

Add all necessary features to get mRNAs for a cdregion feature.

EGeneCheckMode GetGeneCheckMode(void) const

void AddFeatures(CFeat_CI it)

Add all features collected by a CFeat_CI to the tree.

void AddGenesForMrna(const CMappedFeat &mrna_feat, const SAnnotSelector *base_sel=0)

Add all necessary features to get genes for a mRNA feature.

void x_SetParent(CFeatInfo &info, CFeatInfo &parent)

bool AdjustProteinMolInfoToMatchCDS(CMolInfo &molinfo, const CSeq_feat &cds)

AdjustProteinMolInfoToMatchCDS A function to change an existing MolInfo to match a coding region.

CFeatInfo * x_FindInfo(const CSeq_feat_Handle &feat)

bool RemapIds(CSeq_feat &feat, const CTSE_Handle &tse)

void ReassignFeatureIds(const CSeq_entry_EditHandle &entry)

EFeatIdMode

Mode of processing feature ids.

int TFeatLabelFlags

binary OR of FFeatLabelFlags

CMappedFeat GetBestCdsForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree, const SAnnotSelector *base_sel)

bool GivesGeneToChildren(void) const

CFeatTree(void)

Construct empty tree.

@ eBestGene_AllowOverlapped

@ eLocationInFrame_InFrame

@ eLocationInFrame_BadStart

@ eLocationInFrame_BadStop

@ eLocationInFrame_BadStartAndStop

@ fFGL_NoComments

Leave out comments, even as fallbacks.

@ fFGL_NoQualifiers

Leave out qualifiers.

@ fFGL_Content

Include its content if there is any.

@ fFGL_Type

Always include the feature's type.

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 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.

@ 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.

@ eOffset_FromStart

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

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

@ eGetId_Seq_id_BestRank

use CSeq_id::BestRank() as the scoring function

@ fBestFeat_FavorLonger

favor longer features over shorter features

EFeatMapDirection

Mapping direction used when initializing the mapper with a feature.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

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

const CFeat_id & GetId(void) const

const CSeq_feat::TXref & GetXref(void) const

bool GetPseudo(void) const

TClass GetClass(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

void SetDescr(TDescr &v) const

void Remove(void) const

Remove current annot.

const CTSE_Handle & GetTSE_Handle(void) const

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

bool IsSetXref(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

void ClearFeatIds(void)

Clear feature ids.

CSeq_feat_EditHandle AddFeat(const CSeq_feat &new_obj) const

bool IsSetProduct(void) const

virtual const CSeq_loc & GetLocation(void) const

void SetInst(TInst &v) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Get parent bioseq-set handle.

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

void SetFeatId(int id)

Set single feature id.

bool IsProtein(void) const

TInst_Topology GetInst_Topology(void) const

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CSeq_entry_Handle GetParentEntry(void) const

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

bool IsSetClass(void) const

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

void ClearFeatXrefs(void)

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_feat_EditHandle TakeFeat(const CSeq_feat_EditHandle &handle) const

CSeq_annot_EditHandle GetAnnot(void) const

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

bool IsSetQual(void) const

CSeqFeatData::ESubtype GetFeatSubtype(void) const

CSeqFeatData::E_Choice GetFeatType(void) const

bool IsSetPseudo(void) const

bool IsSetInst_Topology(void) const

void Replace(const CSeq_feat &new_feat) const

Replace the feature with new Seq-feat object.

CConstRef< CSeq_annot > GetSeq_annotCore(void) const

bool IsSetData(void) const

CSeq_entry_EditHandle GetParentEntry(void) const

Navigate object tree.

SAnnotSelector & IncludeFeatSubtype(TFeatSubtype subtype)

Include feature subtype in the search.

SAnnotSelector & SetExactDepth(bool value=true)

SetExactDepth() specifies that annotations will be searched on the segment level specified by SetReso...

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetOverlapTotalRange(void)

Check overlapping only of total ranges.

SAnnotSelector & SetSourceLoc(const CSeq_loc &loc)

Set filter for source location of annotations.

const CSeq_loc & GetLocation(void) const

SAnnotSelector & SetOverlapType(EOverlapType overlap_type)

Set overlap type.

SAnnotSelector & SetAdaptiveDepth(bool value=true)

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

SAnnotSelector & SetLimitSeqAnnot(const CSeq_annot_Handle &limit)

Limit annotations to those from the seq-annot only.

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

EOverlapType

Flag to indicate location overlapping method.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

const CSeq_loc & GetProduct(void) const

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

@ eOverlap_Intervals

default - overlapping of individual intervals

@ eOverlap_TotalRange

overlapping of total ranges only

void Reset(void)

Reset reference object.

uint8_t Uint1

1-byte (8-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

int8_t Int1

1-byte (8-bit) signed integer

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.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

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

Compare of a substring with another string.

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

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

#define NCBI_XOBJUTIL_EXPORT

static const char label[]

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

list< CRef< CSubSource > > TSubtype

bool IsSetSubtype(void) const

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

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 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.

bool IsStr(void) const

Check if variant Str is selected.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

const TDb & GetDb(void) const

Get the Db member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetClass(void) const

endeavor which designed this object Check if a value has been assigned to Class data member.

const TClass & GetClass(void) const

Get the Class member data.

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

TId GetId(void) const

Get the variant data.

bool IsGen(void) const

Check if variant Gen is selected.

E_Choice

Choice variants.

const TGen & GetGen(void) const

Get the variant data.

bool IsSetClass(void) const

for ncRNAs, the class of non-coding RNA: examples: antisense_RNA, guide_RNA, snRNA Check if a value h...

const TClass & GetClass(void) const

Get the Class member data.

@ e_not_set

No variant selected.

@ e_Name

for naming "other" type

E_Choice Which(void) const

Which variant is currently selected.

const TDb & GetDb(void) const

Get the variant data.

const TStr & GetStr(void) const

Get the variant data.

@ e_Db

pointer to a restriction site database

@ e_Str

may be unparsable

TXref & SetXref(void)

Assign a value to Xref data member.

bool IsSetOrf(void) const

just an ORF ? Check if a value has been assigned to Orf data member.

bool IsSetComment(void) const

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

vector< CRef< CDbtag > > TDbxref

void ResetPartial(void)

Reset Partial data member.

const TData & GetData(void) const

Get the Data member data.

const TPub & GetPub(void) const

Get the variant data.

bool IsSetData(void) const

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

bool IsSetQual(void) const

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

E_Choice Which(void) const

Which variant is currently selected.

TPsec_str GetPsec_str(void) const

Get the variant data.

bool CanGetQual(void) const

Check if it is safe to call GetQual method.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

TOrf GetOrf(void) const

Get the Orf member data.

bool IsImp(void) const

Check if variant Imp is selected.

const TRegion & GetRegion(void) const

Get the variant data.

const TCit & GetCit(void) const

Get the Cit member data.

E_Choice Which(void) const

Which variant is currently selected.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TQual & GetQual(void) const

Get the Qual member data.

bool IsSetPartial(void) const

incomplete in some way? Check if a value has been assigned to Partial data member.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant 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.

bool IsLocal(void) const

Check if variant Local is selected.

TBond GetBond(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

bool IsGene(void) const

Check if variant Gene is selected.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetData(void) const

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

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.

const TGeneral & GetGeneral(void) const

Get the variant data.

void SetId(TId &value)

Assign a value to Id data member.

const TUser & GetUser(void) const

Get the variant data.

bool IsSetExcept_text(void) const

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

const TDbxref & GetDbxref(void) const

Get the Dbxref member data.

void SetData(TData &value)

Assign a value to Data data member.

const TGiim & GetGiim(void) const

Get the variant data.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool IsSetId(void) const

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

const TProduct & GetProduct(void) const

Get the Product member data.

const TOrg & GetOrg(void) const

Get the variant data.

const TRsite & GetRsite(void) const

Get the variant data.

const TComment & GetComment(void) const

Get the Comment member data.

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.

TSite GetSite(void) const

Get the variant data.

TPartial GetPartial(void) const

Get the Partial member data.

bool IsSetId(void) const

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

const TNon_std_residue & GetNon_std_residue(void) const

Get the variant data.

const TProt & GetProt(void) const

Get the variant data.

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

const TRna & GetRna(void) const

Get the variant data.

TGibb GetGibb(void) const

Get the variant data.

bool IsSetDbxref(void) const

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

bool IsSetProduct(void) const

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

const TVariation & GetVariation(void) const

Get the variant data.

bool IsRna(void) const

Check if variant Rna is selected.

const THet & GetHet(void) const

Get the variant data.

@ e_Het

cofactor, prosthetic grp, etc, bound to seq

@ e_Region

named region (globin locus)

@ e_Seq

to annotate origin from another seq

@ e_Txinit

transcription initiation

@ e_Num

a numbering system

@ e_Pub

publication applies to this seq

@ e_User

user defined structure

@ e_Rsite

restriction site (for maps really)

@ e_Comment

just a comment

@ e_Non_std_residue

non-standard residue here in seq

@ e_General

for use by various databases

@ e_Gibb

geninfo backbone

@ e_Local

for local software use

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

const TRelease & GetRelease(void) const

Get the Release member data.

TId GetId(void) const

Get the Id member data.

bool IsMix(void) const

Check if variant Mix is selected.

bool IsSetRelease(void) const

the release Check if a value has been assigned to Release data member.

ENa_strand

strand of nucleic acid

const TId & GetId(void) const

Get the Id member data.

const TWhole & GetWhole(void) const

Get the variant data.

TFrom GetFrom(void) const

Get the From member data.

bool CanGetTo(void) const

Check if it is safe to call GetTo method.

list< CRef< CSeq_loc > > Tdata

const Tdata & Get(void) const

Get the member data.

bool IsSetStrand(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

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.

const TMix & GetMix(void) const

Get the variant data.

bool IsSetDb(void) const

dbase used in Check if a value has been assigned to Db data member.

const TDb & GetDb(void) const

Get the Db member data.

@ eNa_strand_both_rev

in reverse orientation

@ eNa_strand_both

in forward orientation

@ eClass_nuc_prot

nuc acid and coded proteins

void SetCompleteness(TCompleteness value)

Assign a value to Completeness data member.

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetCompleteness(void) const

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

list< CRef< CSeqdesc > > Tdata

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetAnnot(void) const

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

TNcbieaa & SetNcbieaa(void)

Select the variant.

bool IsSetBiomol(void) const

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

const TAnnot & GetAnnot(void) const

Get the Annot member data.

bool IsSetInst(void) const

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

const TNcbistdaa & GetNcbistdaa(void) const

Get the variant data.

TBiomol GetBiomol(void) const

Get the Biomol member data.

void SetBiomol(TBiomol value)

Assign a value to Biomol data member.

const TFtable & GetFtable(void) const

Get the variant data.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

const TData & GetData(void) const

Get the Data member data.

list< CRef< CSeq_annot > > TAnnot

const TPub & GetPub(void) const

Get the Pub member data.

void SetDefaultCompleteness(void)

Assign default value to Completeness data member.

TIupacaa & SetIupacaa(void)

Select the variant.

@ eCompleteness_complete

complete biological entity

@ eCompleteness_no_left

missing 5' or NH3 end

@ eCompleteness_no_right

missing 3' or COOH end

@ eCompleteness_no_ends

missing both ends

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Ncbistdaa

consecutive codes for std aas

@ e_Iupacaa

IUPAC 1 letter amino acid code.

@ e_not_set

No variant selected.

const TId & GetId(void) const

Get the Id member data.

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 IsSetName(void) const

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

unsigned int

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

constexpr auto sort(_Init &&init)

constexpr bool empty(list< Ts... >) noexcept

double value_type

The numeric datatype used by the parser.

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

static const sljit_gpr r1

static const sljit_gpr r2

bool m_DoesNotNeedChildren

TChildList m_ChildrenCandidates

bool operator()(const CFeatTree::CFeatInfo *f1, const CFeatTree::CFeatInfo *f2) const

bool operator()(const SBestInfo &info1, const SBestInfo &info2) const

CDisambiguator::TChildren::const_iterator TChild

bool operator()(const TChild &c1, const TChild &c2) const

CSeqFeatData::ESubtype m_StartType

CSeqFeatData::ESubtype m_CurrentType

bool OverlapByIntervals() const

const CSeqFeatData::ESubtype * GetMultiParentTypes() const

STypeLink & operator++(void)

bool CanHaveCommonGene(void) const

CSeqFeatData::ESubtype m_ParentType

bool CanHaveGeneParent(void) const

bool operator!(void) const

STypeLink(CSeqFeatData::ESubtype subtype=CSeqFeatData::eSubtype_imp, CSeqFeatData::ESubtype start=CSeqFeatData::eSubtype_bad)

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