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

( ! obj1.

() ) {

( subtypevalue1 != subtypevalue2 ) {

( name1 != name2 ) {

( ! obj1.

() ) {

obj1->

( *obj2 );

( ! obj1.

() ) {

obj1->

( *obj2 );

);

(

, entry, bsh, useSeqEntryIndexing, topLevelSeqEntryContext, doNuc, doProt);

useSeqEntryIndexing,

doNuc,

doProt)

(( bsh.

() && doNuc ) || ( bsh.

() && doProt )) {

doNuc,

doProt)

( ; seq_iter; ++seq_iter ) {

(prev_seq, this_seq, next_seq, topLevelSeqEntryContext);

next_seq = *seq_iter;

(prev_seq, this_seq, next_seq, topLevelSeqEntryContext);

(it->IsSet() && it->GetSet().IsSetClass() &&

);

);

(topLevelSeqEntryContext ? &*topLevelSeqEntryContext :

)));

missing =

;

(!

.IsCrossKingdom())

;

(!

.IsRSUniqueProt())

;

src->

().SetTaxname(

);

src->

().SetOrgname().SetLineage(

);

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

( ( !

.CanGetTLSeqEntryCtx() ||

.GetTLSeqEntryCtx().GetCanSourcePubsBeFused() ) &&

(pubdesc) ) {

& comment = pubdesc.

();

( ! it.GetSeq_entry_Handle().HasParentEntry() ) {

annot_it; ++annot_it) {

( !annot_it->Seq_annot_IsSetDesc() ) {

annot_it->Seq_annot_GetDesc().Get()) {

( !(*it)->IsPub() ) {

(

smit(seqmap, &scope, mapsel); smit; ++smit) {

( ; fci; ++fci) {

const CPubdesc& pubdesc = sd.GetPub();

if ( s_FilterPubdesc(pubdesc, *m_Current) ) {

annot_it; ++annot_it) {

( !annot_it->Seq_annot_IsSetDesc() ) {

annot_it->Seq_annot_GetDesc().Get()) {

( !(*it)->IsPub() ) {

desc->SetPub(

&

((*it)->GetPub()));

( ; fci; ++fci) {

& sf = fci->GetOriginalFeature();

(m_Current->GetSubmitBlock()) {

( primary_seq_id ) {

( potential_cds_seq ) {

cds_seq = potential_cds_seq;

( (*coreSeqSet_iter)->IsSeq() ) {

* coreSeqId = (*coreSeqSet_iter)->GetSeq().GetFirstId();

( potential_cds_seq ) {

cds_seq = potential_cds_seq;

& feat = it->GetOriginalFeature();

( ! it.GetSeq_entry_Handle().HasParentEntry() ) {

(

.UsingSeqEntryIndex() ) {

item.

( *ref );

(

.ShowGBBSource() ) {

(

.ShowAnnotCommentAsCOMMENT() ) {

( !com->Skip() ) {

( !gsdb_comment->Skip() ) {

( setCommentsSeen.

((*com_iter)->GetCommentList()) == setCommentsSeen.

() ) {

setCommentsSeen.

((*com_iter)->GetCommentList());

newComments.push_back(*com_iter);

(

idx = 0; idx < (

.size() - 1); ++idx ) {

(*it)->RemovePeriodAfterURL();

(gsdb && it !=

) {

item.

( *it );

TUnverifiedElem sc_unverified_map[] = {

},

},

}

vector<string> arr_type_string;

( TUnverifiedMap, map_iter, sc_UnverifiedMap ) {

( (

.GetUnverifiedType() & map_iter->first) != 0 ) {

arr_type_string.push_back(map_iter->second);

(arr_type_string.empty() && !is_contaminated) {

(!arr_type_string.empty()) {

+=

;

(

ii = 0; ii < arr_type_string.size(); ++ii ) {

}

( ii == (arr_type_string.size() - 1) ) {

(is_contaminated) {

(arr_type_string.size() > 0) {

+=

;

(!is_unannotated) {

=

;

item->SetNeedPeriod(

);

item->SetNeedPeriod(

);

sAuthorizedAccess =

genome_build_number =

&

= **id_iter;

(

.Which() ) {

(

.IsRSCompleteGenomic() ) {

( !genome_build_number.empty() &&

!has_ref_track_status

(

.IsRSContig() ||

.IsRSIntermedWGS() ) {

(

.IsEncode() ) {

}

( !has_ref_track_status

) {

(

.IsRSPredictedProtein() ||

.IsRSPredictedMRna() ||

.IsRSPredictedNCRna() ||

.IsRSWGSProt() )

( !

.empty() ) {

item->SetNeedPeriod(

);

(

.IsRSUniqueProt() ) {

( !

.empty() ) {

& dbtag =

.GetGeneral();

file_id = &(

.GetGeneral().GetTag());

local_id = &(

.GetLocal());

(

.IsTPA() ||

.IsGED() ) {

(

.Config().IsModeGBench() ||

.Config().IsModeDump() ) {

did_tpa =

, did_ref_track =

, did_genome =

;

( !

.empty() ) {

( !

.Config().HideBankItComment() ) {

( !

.empty() ) {

( !did_ref_track ) {

( !

.empty() ) {

did_ref_track =

;

( !did_genome ) {

( (*hist_iter) && (*hist_iter)->IsGi() && (*hist_iter)->GetGi() == gi ) {

(

.CanGetDate() && !

.GetIds().empty() &&

(

.CanGetDate() && !

.GetIds().empty() &&

( !

.empty() ) {

( !

.IsWGSMaster() ||

.GetWGSMasterName().empty() ) {

( !

.empty() ) {

( !

.empty() ) {

( !

.empty() ) {

(!

.ShowGBBSource()) {

& gbb = it->GetGenbank();

comment =

+ gbb.

();

(

.UsePDBCompoundForComment()) {

(

id_handle :

.GetHandle().GetId()) {

(typ.

()) {

= typ.

();

chs1 = desc1->

();

chs2 = desc2->

();

(str1.length() > 0 && str2.length() > 0) {

issc1 = (

) (str1 ==

);

issc2 = (

) (str2 ==

);

(issc1 && issc2) {

(val1 < val2);

vector<CConstRef<CSeqdesc> > vdesc;

vdesc.push_back(dsc);

(

ii = 0; ii < vdesc.size(); ii++) {

list<string>* keywords =

;

(list<string>, kwd, *keywords) {

(

.IsRefSeq() &&

( !

.empty() ) {

( ; annot_ci; ++annot_ci ) {

( ! descr.

() ) {

( ! firstGenAnnotSCAD &&

.IsNcbiGenomes() &&

.GetHandle().IsSetInst_Ext() &&

.GetHandle().GetInst_Ext().IsDelta() &&

.GetHandle().GetInst_Ext().GetDelta().IsSet() )

( ! (*ext_iter)->IsLoc() ) {

& loc = (*ext_iter)->GetLoc();

( firstGenAnnotSCAD ) {

firstGenAnnotSCAD;

firstGenAnnotSCAD;

( ; curr_entry_h ; curr_entry_h = curr_entry_h.

() ) {

( ; annot_ci; ++annot_ci ) {

( ! annot_descr.

() ) {

( ! (*descr_iter)->IsUser() ) {

& descr_user = (*descr_iter)->GetUser();

( prefix_field &&

( prefix_field &&

from = ( from >= 1 ? from : 1 );

loop = (

) (

.IsSP() || (

.IsCrossKingdom() &&

.IsRSUniqueProt()));

sf->SetObject(*dit);

(!loop && okay) {

(; smit; ++smit) {

(; src_it; ++src_it) {

(

.IsProt() ) {

( !

.IsProt() ) {

.GetLocation().GetTotalRange(),

( loc->

().

().size() < 2 ) {

need_to_normalize =

;

( force_adding_nulls ) {

need_to_normalize =

;

saw_multiple_non_nulls_in_a_row =

;

last_was_null =

;

any_null_seen =

;

( ; loc_ci ; ++loc_ci ) {

last_was_null =

;

any_null_seen =

;

( last_was_null ) {

last_was_null =

;

saw_multiple_non_nulls_in_a_row =

;

need_to_normalize = ( any_null_seen && saw_multiple_non_nulls_in_a_row );

( ! need_to_normalize ) {

( ; loc_ci ; ++loc_ci ) {

( ! mix_data.empty() ) {

mix_data.push_back( null_loc );

mix_data.push_back( loc_piece );

( srcs.size() < 2 ) {

& focus_seq_loc = focus->GetLoc();

unique_ptr<CSeq_loc> copyOfOriginalSeqLocOfFocus(

() );

copyOfOriginalSeqLocOfFocus->Assign( focus_seq_loc );

(it != srcs.begin()) {

( focus->GetLoc().GetTotalRange().GetLength() == 0 ) {

focus->SetLoc( *copyOfOriginalSeqLocOfFocus );

copyOfOriginalSeqLocOfFocus.release();

focus_loc_iter = focus->GetLoc().begin();

( focus_loc_iter != focus->GetLoc().end() ) {

( focus_loc_iter != focus->GetLoc().end() ) {

focus->SetLoc( *new_focus );

(sfp1->WasDesc() && !sfp2->WasDesc()) {

}

(!sfp1->WasDesc() && sfp2->WasDesc()) {

( srcs.empty() ) {

(srcs.front()->IsFocus() && !srcs.front()->IsSynthetic()) {

( srcs.front()->GetLoc().GetTotalRange().GetLength() == 0 &&

item.

( *it );

( srcs.size() < 2 ) {

sourcePubFuse =

;

( ! seqId.

() ) {

( seqId->

() ) {

sourcePubFuse =

;

sourcePubFuse =

;

( ! sourcePubFuse ) {

TSourceFeatSet::iterator item_outer = srcs.begin();

( ; item_outer != srcs.end(); ++item_outer ) {

( item_outer->IsNull() ) {

TSourceFeatSet::iterator item_inner = item_outer;

( item_inner != srcs.end() ) {

( item_inner->IsNull() ) {

((*item_outer)->GetLoc(), (*item_inner)->GetLoc(),

(*item_outer)->SetLoc(*merged_loc);

item_inner->Release();

TSourceFeatSet::iterator copy_iter = srcs.begin();

( ; copy_iter != srcs.end(); ++copy_iter ) {

( ! copy_iter->IsNull() ) {

newSrcs.push_back( *copy_iter );

srcs.swap( newSrcs );

( taxname1 != taxname2 ) {

( comment1 != comment2 ) {

( orgmod1.size() != orgmod2.size() ) {

( ! equal( orgmod1.begin(), orgmod1.end(),

( db1.size() != db2.size() ) {

( ! equal( db1.begin(), db1.end(),

( subtype1.size() != subtype2.size() ) {

( ! equal( subtype1.begin(), subtype1.end(),

locations_overlap_or_touch =

( ! locations_overlap_or_touch ) {

(

.IsNuc()) {

(!

.GetAnnotSelector()) {

showOutOfBoundsFeats =

.Config().ShowOutOfBoundsFeats();

is_part =

.IsPart();

is_small_genome_set =

.GetSGS();

( showOutOfBoundsFeats && ! is_part && ! is_small_genome_set ) {

any_piece_is_on_bioseq =

;

( ! any_piece_is_on_bioseq ) {

any_piece_is_on_bioseq =

;

(

.IsSeqIdInSameTopLevelSeqEntry(it.GetSeq_id()) ) {

( ! first_non_far ) {

( ! first_non_far || ! any_piece_is_on_bioseq ) {

( is_small_genome_set ) {

first_is_on_bioseq = (

== first_non_far &&

( first_is_on_bioseq ) {

.IsSeqIdInSameTopLevelSeqEntry(

.GetSeq_id()) )

(

!= first_non_far &&

part_to_check = ( bMinus ? first_non_far : last_non_far );

endsOnThisBioseq = ( part_to_check &&

endsOnThisBioseq;

( endsOnThisBioseq ) {

.IsInGPS() && !

.IsInNucProt() &&

.Config().CopyCDSFromCDNA();

( !

.IsDelta() ) {

(

.Config().HideGapFeatures()) {

(1,

);

gapDepth =

.Config().GetGapDepth();

kRegularGap =

;

kAssemblyGap =

;

( pSeqLiteral && pSeqLiteral->IsSetSeq_data() )

& seq_data = pSeqLiteral->GetSeq_data();

( seq_data.

() ) {

pGap = &seq_data.

();

& sType = gap_mod_text.

;

bIsAssemblyGap = ( ! sType.empty() || ! sEvidence.empty() );

& sFeatName = ( bIsAssemblyGap ? kAssemblyGap : kRegularGap );

(pos, end_pos,

, sFeatName, sType, sEvidence) :

(pos, end_pos,

, sFeatName, sType, sEvidence,

vector<string>& evidence,

isUnknownLength,

isAssemblyGap,

kRegularGap =

;

kAssemblyGap =

;

bIsAssemblyGap = ( ! gap_type.empty() || ! evidence.empty() );

& sFeatName = ( bIsAssemblyGap ? kAssemblyGap : kRegularGap );

(gap_start, gap_end,

, sFeatName, gap_type, evidence) :

(gap_start, gap_end,

, sFeatName, gap_type, evidence,

feats_have_same_structure =

( ! feats_have_same_structure ) {

( f1_annot && f2_annot ) {

( (f1_annot == f2_annot) ||

(loc_label.size() > 100) {

loc_label.replace(97,

,

);

desc.c_str();

(feat.

().find_last_not_of(

) !=

& comment =

pair<const char*, CSeqFeatData::ESite>

;

kMaxPair =

(

) /

(

);

(

= 0;

< kMaxPair; ++

) {

.SetData().SetSite(

[

].second);

.SetData().SetSite(

[

].second);

.SetData().SetRegion(x);

( ; it; ++it ) {

( featIsGap && (feat_start == gap_start) && (feat_end == gap_end) ) {

( feat_start > gap_start ) {

temp_annot->

().SetFtable().push_back(feat);

trimmed_feat = sequence::CFeatTrim::Apply(feat, range);

(name ==

|| name ==

|| name ==

);

vector<CRef<CGapIndex>>& gaps = bsx->

();

gap_data.next_gap = 0;

(gap_data.num_gaps > 0 && !

.Config().HideGapFeatures()) {

load_cdd =

;

(!

.Config().HideCDDFeatures()) {

(

.Config().GetPolicy()) {

load_cdd =

.Config().ShowCDDFeatures();

(

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

cdd_ids.push_back(cds_it->GetProductId());

gaps, &gap_data, showGapsOfSizeZero, bsx](

& sfx) {

CSeq_id_Handle rna =

sequence::GetIdHandle(original_feat.GetProduct(), &scope);

CSeq_id_Handle prot =

sequence::GetIdHandle(children.front().GetProduct(),

CBioseq_Handle rna_bsh;

CBioseq_Handle prot_bsh;

GetResolveOrder(scope,

(( !

.Config().IsFormatFTable() ||

.Config().ShowFtablePeptides() )) {

( feat_start > feat_end ) {

feat_start -= loc_len;

has_gap = gap_data.has_gap;

gap_start = gap_data.gap_start;

gap_end = gap_data.gap_end - 1;

(has_gap && gap_start < feat_start) {

noGapSizeProblem = ( showGapsOfSizeZero || (gap_start <= gap_end + 1) );

( noGapSizeProblem && ! gapMatch ) {

item.

(

(gap_data.gap_start, gap_data.gap_end, gap_data.gap_length, gap_data.gap_type,

gap_data.gap_evidence, gap_data.is_unknown_length, gap_data.is_assembly_gap,

) );

(gap_data.next_gap < gap_data.num_gaps) {

has_gap = gap_data.has_gap;

gap_start = gap_data.gap_start;

gap_end = gap_data.gap_end;

gap_data.has_gap =

;

(gap_end > feat_end) {

}

(gap_data.next_gap < gap_data.num_gaps) {

has_gap = gap_data.has_gap;

gap_start = gap_data.gap_start;

gap_end = gap_data.gap_end;

gap_data.has_gap =

;

(( !

.Config().IsFormatFTable() ||

.Config().ShowFtablePeptides() )) {

<<

<< e <<

);

<<

<< e <<

);

(gap_data.has_gap) {

noGapSizeProblem = ( showGapsOfSizeZero || (gap_data.gap_start <= gap_data.gap_end) );

( noGapSizeProblem

) {

item.

(

(gap_data.gap_start, gap_data.gap_end, gap_data.gap_length, gap_data.gap_type,

gap_data.gap_evidence, gap_data.is_unknown_length, gap_data.is_assembly_gap,

) );

(gap_data.next_gap < gap_data.num_gaps) {

gap_data.has_gap =

;

.GetFeatTree().AddFeatures(it);

vector<CMappedFeat> children =

.GetFeatTree().GetChildren(*it);

(children.size() == 1 &&

children.front().IsSetProduct()) {

(( !

.Config().IsFormatFTable() ||

.Config().ShowFtablePeptides() )) {

( feat_start > feat_end ) {

feat_start -= loc_len;

( feat_start >= gap_start ) {

noGapSizeProblem = ( showGapsOfSizeZero || (gap_start <= gap_end) );

(( !

.Config().IsFormatFTable() ||

.Config().ShowFtablePeptides() )) {

<<

<< e <<

);

<<

<< e <<

);

s_UniqueIdOffset = 0;

seq->SetId().push_back(s_MakeUniqueId(scope));

seq->SetInst().Assign(bsh.

());

seq->SetInst().ResetSeq_data();

seq->SetInst().ResetExt();

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

seq->SetInst().SetExt().SetDelta().Set().push_back(element);

any_change =

;

new_loc->Assign(loc);

&

= it.GetSeq_id();

(

.

(temporary)) {

it.SetSeq_id(

);

new_loc->

(*it.MakeSeq_loc());

seq_id.

( *

.GetHandle().GetSeqId() );

old_loc.

().SetId( seq_id );

old_loc.

().SetFrom( 0 );

old_loc.

().SetTo( new_len - 1 );

slice_mapper;

isWhole =

.GetLocation().IsWhole();

(

.GetMasterLocation()) {

loc.

(*

.GetMasterLocation());

loc.

(*

.GetHandle().GetRangeSeq_loc(0, 0));

(

fi(bh, range, as); fi; ++fi ) {

start = fi->GetLocation().GetTotalRange().GetFrom();

stop = fi->GetLocation().GetTotalRange().GetTo();

( to >= start && from <= stop ) {

& ft = fi->GetMappedFeature();

.GetFeatTree().AddFeatures(it);

vector<CMappedFeat> children =

.GetFeatTree().GetChildren(*it);

(children.size() == 1 &&

children.front().IsSetProduct()) {

(( !

.Config().IsFormatFTable() ||

.Config().ShowFtablePeptides() )) {

( feat_start > feat_end ) {

feat_start -= loc_len;

( feat_start >= gap_start ) {

noGapSizeProblem = ( showGapsOfSizeZero || (gap_start <= gap_end) );

( noGapSizeProblem

) {

(( !

.Config().IsFormatFTable() ||

.Config().ShowFtablePeptides() )) {

<<

<< e <<

);

<<

<< e <<

);

.GetFeatTree().AddFeatures(it);

vector<CMappedFeat> children =

.GetFeatTree().GetChildren(*it);

(children.size() == 1 &&

children.front().IsSetProduct()) {

feat_loc = s_FixId(*feat_loc, *(

.GetBioseqIds().front()), *(

->GetId().front()));

(( !

.Config().IsFormatFTable() ||

.Config().ShowFtablePeptides() )) {

(( !

.Config().IsFormatFTable() ||

.Config().ShowFtablePeptides() )) {

<<

<< e <<

);

<<

<< e <<

);

(

.GetLocation().IsWhole() ) {

(

.UsingSeqEntryIndex() ) {

(

.UsingSeqEntryIndex() ) {

( ; it; ++it ) {

(

.GetAnnotSelector()) {

selp = &

.SetAnnotSelector();

(

.GetMasterLocation()) {

loc.

(*

.GetMasterLocation());

loc.

(*

.GetHandle().GetRangeSeq_loc(0, 0));

(

.GetLocation().IsWhole()) {

(

.IsProt() ) {

(cds_prod_seq_id) {

prod_bioseq_handle =

.GetScope().GetBioseqHandle( *cds_prod_seq_id );

( prod_bioseq_handle ) {

( cds_prod->

().

() >= bioseq_len ) {

cds_prod->

().SetTo( bioseq_len - 1 );

.GetFeatTree().AddFeatures(it);

(

.GetAnnotSelector()) {

selp = &

.SetAnnotSelector();

(

.GetMasterLocation()) {

loc.

(*

.GetMasterLocation());

loc.

(*

.GetHandle().GetRangeSeq_loc(0, 0));

(

.IsProt() ) {

(cds_prod_seq_id) {

prod_bioseq_handle =

.GetScope().GetBioseqHandle( *cds_prod_seq_id );

( prod_bioseq_handle ) {

( cds_prod->

().

() >= bioseq_len ) {

cds_prod->

().SetTo( bioseq_len - 1 );

.GetFeatTree().AddFeatures(it);

( ! pDestLoc->

() ) {

( ! srcLoc.

() ) {

( ! featLoc.

() ) {

destInt.

( featInt.

() - uRawFrom );

destInt.

( destInt.

() + frame -1 );

( 3 + featInt.

() - destInt.

() < 6 ) {

(!feat.GetData().IsCdregion() || !feat.CanGetProduct()) {

.GetFeatTree().AddFeatures( it );

( ; it; ++it ) {

x_GiveOneResidueIntervalsBogusFuzz(*loc);

x_RemoveBogusFuzzFromIntervals(*loc);

(!loc || loc->

()) {

( slice_mapper && loc ) {

( mapped_loc->

() ) {

(!feat.GetData().IsCdregion() || !feat.CanGetProduct()) {

.GetFeatTree().AddFeatures( it );

( ; it; ++it ) {

x_GiveOneResidueIntervalsBogusFuzz(*loc);

x_RemoveBogusFuzzFromIntervals(*loc);

(!loc || loc->

()) {

( slice_mapper && loc ) {

( mapped_loc->

() ) {

( loc.

() ) {

( loc.

() ) {

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.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Seq-loc and seq-align mapper exceptions.

const string & GetTaxname(void) const

bool IsSetTaxname(void) const

CBioseq_Handle & GetHandle(void)

CScope & GetScope(void) const

@ fUnreviewed_Unannotated

SAnnotSelector & SetAnnotSelector(void)

const CFlatFileConfig & Config(void) const

const CSubmit_block * GetSubmitBlock(void) const

CSeq_inst::TRepr GetRepr(void) const

CSeq_id * GetPrimaryId(void)

const CSeq_entry_Handle & GetTopLevelEntry(void) const

TReferences & SetReferences(void)

void SetRefCache(vector< string > *rc)

const CSeq_loc & GetLocation(void) const

@ fUnverified_Contaminant

@ fUnverified_SequenceOrAnnotation

@ fUnverified_Misassembled

const vector< CRef< CGapIndex > > & GetGapIndices(void)

void GetSelector(SAnnotSelector &sel)

size_t IterateDescriptors(Fnc m)

size_t IterateFeatures(Fnc m)

const CSeq_loc & GetLoc(void) const

bool operator()(const CRef< CDbtag > &obj1, const CRef< CDbtag > &obj2)

bool Match(const CDbtag &dbt2) const

CSeqdesc::E_Choice GetType(void) const

const CSeqdesc & GetSeqDesc(void) const

static CRef< CSeq_feat > Apply(const CSeq_feat &feat, const CRange< TSeqPos > &range)

CSeq_feat_Handle GetSeqFeatHandle(void) const

const CMappedFeat GetMappedFeat(void) const

CConstRef< CSeq_loc > GetMappedLocation(void) const

const CMappedFeat & GetFeat(void) const

const CSeq_loc & GetLoc(void) const

bool IsPolicyInternal(void) const

bool IsStyleSegment(void) const

bool CopyGeneToCDNA(void) const

bool HideRemoteImpFeatures(void) const

bool HideGapFeatures(void) const

bool HideImpFeatures(void) const

bool DisableReferenceCache(void) const

bool ShowCDDFeatures(void) const

bool IsPolicyFtp(void) const

bool UseSeqEntryIndexer(void) const

bool ShowContigFeatures(void) const

bool HideEmptySource(void) const

bool ShowContigSources(void) const

bool ForGBRelease(void) const

bool IsPolicyGenomes(void) const

bool LatestGeneRIFs(void) const

bool IsFormatFTable(void) const

bool OnlyGeneRIFs(void) const

bool HideCDSProdFeatures(void) const

bool HideSNPFeatures(void) const

bool HideMiscFeatures(void) const

bool HideCDDFeatures(void) const

bool ShowFtablePeptides(void) const

bool IsModeRelease(void) const

bool IsModeDump(void) const

bool DisableAnnotRefs(void) const

bool HideExonFeatures(void) const

bool IsShownGenbankBlock(FGenbankBlocks fTGenbankBlocksMask) const

bool IsStyleNormal(void) const

bool IsStyleContig(void) const

bool HideGeneRIFs(void) const

bool HideIntronFeatures(void) const

const CRef< CSeqEntryIndex > GetSeqEntryIndex(void) const

bool UsingSeqEntryIndex(void) const

const CSeq_loc * GetLocation(void) const

void AddSection(TSection &section)

void x_WGSComment(CBioseqContext &ctx) const

void x_RegionComments(CBioseqContext &ctx) const

virtual void Gather(CFlatFileContext &ctx, CFlatItemOStream &os, bool doNuc=true, bool doProt=true) const

void x_GatherFeatures(void) const

void x_GatherFeaturesOnWholeLocationIdx(const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void x_TSAComment(CBioseqContext &ctx) const

void x_GBBSourceComment(CBioseqContext &ctx) const

void x_FlushComments(void) const

void x_GatherComments(void) const

CRef< CFlatItemOStream > m_ItemOS

void x_NameComments(CBioseqContext &ctx) const

CRef< CBioseqContext > m_Current

virtual void x_GatherFeaturesOnLocation(const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void x_FeatComments(CBioseqContext &ctx) const

const ICanceled * m_pCanceledCallback

void x_GatherReferences(void) const

void x_MaplocComments(CBioseqContext &ctx) const

void x_GetFeatsOnCdsProductIdx(const CSeq_feat &feat, CBioseqContext &ctx, CRef< CSeq_loc_Mapper > slice_mapper, CConstRef< CFeatureItem > cdsFeatureItem=CConstRef< CFeatureItem >()) const

CBioseqContext::TReferences TReferences

void x_GatherSourceFeatures(void) const

void x_RefSeqGenomeComments(CBioseqContext &ctx) const

virtual CFeatureItem * x_NewFeatureItem(const CMappedFeat &feat, CBioseqContext &ctx, const CSeq_loc *loc, CRef< feature::CFeatTree > ftree, CFeatureItem::EMapped mapped=CFeatureItem::eMapped_not_mapped, bool suppressAccession=false, CConstRef< CFeatureItem > parentFeatureItem=CConstRef< CFeatureItem >()) const

void x_IdComments(CBioseqContext &ctx, EGenomeAnnotComment eGenomeAnnotComment) const

bool x_BiosourcesEqualForMergingPurposes(const CSourceFeatureItem &src1, const CSourceFeatureItem &src2) const

@ eGenomeAnnotComment_Yes

void x_GatherFeaturesOnRangeIdx(const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void x_RemoveExcessNewlines(void) const

void x_GatherSequence(void) const

vector< string > & RefCache(void) const

void x_GatherCDSReferences(TReferences &refs) const

CConstRef< CUser_object > m_FirstGenAnnotSCAD

virtual void x_GatherSeqEntry(CFlatFileContext &ctx, CRef< CTopLevelSeqEntryContext > topLevelSeqEntryContext=CRef< CTopLevelSeqEntryContext >(), bool doNuc=true, bool doProt=true) const

void x_HistoryComments(CBioseqContext &ctx) const

deque< TSFItem > TSourceFeatSet

void x_MergeEqualBioSources(TSourceFeatSet &srcs) const

void x_CollectSourceDescriptors(const CBioseq_Handle &bh, CBioseqContext &ctx, TSourceFeatSet &srcs) const

void x_AddGSDBComment(const CDbtag &dbtag, CBioseqContext &ctx) const

void x_UnorderedComments(CBioseqContext &ctx) const

void x_TLSComment(CBioseqContext &ctx) const

CRef< feature::CFeatTree > m_Feat_Tree

CRef< CFlatFileContext > m_Context

vector< string > m_RefCache

CSeq_entry_Handle m_TopSEH

void x_RefSeqComments(CBioseqContext &ctx, EGenomeAnnotComment eGenomeAnnotComment) const

void x_UnverifiedComment(CBioseqContext &ctx) const

virtual void x_GatherBioseq(const CBioseq_Handle &prev_seq, const CBioseq_Handle &this_seq, const CBioseq_Handle &next_seq, CRef< CTopLevelSeqEntryContext > topLevelSeqEntryContext=CRef< CTopLevelSeqEntryContext >()) const

void x_DescComments(CBioseqContext &ctx) const

void x_BasemodComment(CBioseqContext &ctx) const

virtual void x_DoMultipleSections(const CBioseq_Handle &seq) const

static void x_GiveOneResidueIntervalsBogusFuzz(CSeq_loc &loc)

void x_StructuredComments(CBioseqContext &ctx) const

vector< CRef< CCommentItem > > TCommentVec

CConstRef< CUser_object > x_GetAnnotDescStrucCommentFromBioseqHandle(CBioseq_Handle bsh) const

static void x_RemoveBogusFuzzFromIntervals(CSeq_loc &loc)

void x_HTGSComments(CBioseqContext &ctx) const

static CFlatGatherer * New(CFlatFileConfig::TFormat format)

virtual void x_DoSingleSection(CBioseqContext &ctx) const =0

void x_AddComment(CCommentItem *comment) const

void x_GetFeatsOnCdsProduct(const CSeq_feat &feat, CBioseqContext &ctx, CRef< CSeq_loc_Mapper > slice_mapper, CConstRef< CFeatureItem > cdsFeatureItem=CConstRef< CFeatureItem >()) const

virtual ~CFlatGatherer(void)

void x_CollectBioSourcesOnBioseq(const CBioseq_Handle &bh, const TRange &range, CBioseqContext &ctx, TSourceFeatSet &srcs) const

const CFlatFileConfig & Config(void) const

void x_CollectBioSources(TSourceFeatSet &srcs) const

void x_GatherFeaturesIdx(void) const

void x_CollectSourceFeatures(const CBioseq_Handle &bh, const TRange &range, CBioseqContext &ctx, TSourceFeatSet &srcs) const

void x_AnnotComments(CBioseqContext &ctx) const

void x_AuthorizedAccessComment(CBioseqContext &ctx) const

void x_CopyCDSFromCDNA(const CSeq_feat &feat, CBioseqContext &ctx) const

void x_GatherFeaturesOnRange(const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void x_SubtractFromFocus(TSourceFeatSet &srcs) const

void x_GatherSourceOrganism(void) const

void x_GatherFeaturesOnWholeLocation(const CSeq_loc &loc, SAnnotSelector &sel, CBioseqContext &ctx) const

void x_RemoveDupComments(void) const

void x_UnreviewedComment(CBioseqContext &ctx) const

CConstRef< CUser_object > x_PrepareAnnotDescStrucComment(CBioseqContext &ctx) const

void x_GatherAlignments(void) const

void x_GatherReferencesIdx(const CSeq_loc &loc, TReferences &refs) const

void x_MapComment(CBioseqContext &ctx) const

CBioseqContext * GetContext(void)

bool operator()(const CRef< COrgMod > &obj1, const CRef< COrgMod > &obj2)

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

static void Rearrange(TReferences &refs, CBioseqContext &ctx)

bool DistributedReferences(void)

CRef< CBioseqIndex > GetBioseqIndex(void)

@ eSubtype_transit_peptide_aa

@ eSubtype_non_std_residue

@ eSubtype_sig_peptide_aa

@ eSubtype_mat_peptide_aa

namespace ncbi::objects::

CConstRef< CDbtag > GetNamedDbxref(const CTempString &db) const

Return a specified DB xref.

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

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

Base class for all serializable objects.

const CBioSource & GetSource(void) const

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

bool operator()(const CRef< CSubSource > &obj1, const CRef< CSubSource > &obj2)

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

string Tag(const string &name, int value)

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

static const TPair sc_Pairs[]

SStaticPair< const char *, const char * > TPair

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() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

static void s_GiveOneResidueIntervalsBogusFuzz_Helper(CSeq_interval &interval)

static bool s_LocationsOverlap(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *p_scope)

bool s_FilterPubdesc(const CPubdesc &pubdesc, CBioseqContext &ctx)

static bool s_CopyCDSFromCDNA(CBioseqContext &ctx)

static bool s_SeqLocEndsOnBioseq(const CSeq_loc &loc, CBioseqContext &ctx, EEndsOnBioseqOpt mode, CSeqFeatData::E_Choice feat_type)

static string s_GetFeatDesc(const CSeq_feat_Handle &feat)

CRef< CSeq_loc_Mapper > s_MakeSliceMapper(const CSeq_loc &loc, CBioseqContext &ctx)

static bool s_GiInCSeq_hist_ids(const TGi gi, const CSeq_hist_rec_Base::TIds &ids)

static CRef< CGapItem > s_NewGapItem(CSeqMap_CI &gap_it, CBioseqContext &ctx)

static bool s_IsCDD(const CSeq_feat_Handle &feat)

@ eEndsOnBioseqOpt_AnyPartOfSeqLoc

@ eEndsOnBioseqOpt_LastPartOfSeqLoc

CSeqMap_CI s_CreateGapMapIter(const CSeq_loc &loc, CBioseqContext &ctx)

static string s_GetUserObjectTypeOrClass(const CUser_object &uop)

static bool s_HasSegments(const CBioseq_Handle &seq)

static CMappedFeat s_GetTrimmedMappedFeat(const CSeq_feat &feat, const CRange< TSeqPos > &range, CScope &scope)

static void s_CleanCDDFeature(const CSeq_feat &feat)

static void s_RemoveBogusFuzzFromIntervals_Helper(CSeq_interval &interval)

bool s_HasRefTrackStatus(const CBioseq_Handle &bsh)

static CConstRef< CSeq_loc > s_NormalizeNullsBetween(CConstRef< CSeq_loc > loc, bool force_adding_nulls=false)

static int s_StrucCommOrder(const string &str)

static bool s_NsAreGaps(const CBioseq_Handle &seq, CBioseqContext &ctx)

void s_FixIntervalProtToCds(const CSeq_feat &srcFeat, const CSeq_loc &srcLoc, CRef< CSeq_loc > pDestLoc)

static bool s_LocationsTouch(const CSeq_loc &loc1, const CSeq_loc &loc2)

static void s_SetGapIdxData(SGapIdxData &gapdat, const vector< CRef< CGapIndex >> &gaps)

static bool s_SeqDescCompare(const CConstRef< CSeqdesc > &desc1, const CConstRef< CSeqdesc > &desc2)

static bool s_IsSegmented(const CBioseq_Handle &seq)

static bool s_IsCircularTopology(CBioseqContext &ctx)

static CMappedFeat s_GetMappedFeat(CRef< CSeq_feat > &feat, CScope &scope)

static bool s_ContainsGaps(const CSeq_loc &loc)

bool s_CoincidingGapFeatures(CFeat_CI it, const TSeqPos gap_start, const TSeqPos gap_end)

bool s_IsJustUids(const CPubdesc &pubdesc)

bool s_BioSeqHasContig(const CBioseq_Handle &seq, CFlatFileContext &ctx)

static bool s_IsDuplicateFeatures(const CSeq_feat_Handle &f1, const CSeq_feat_Handle &f2)

SAnnotSelector s_GetCdsProductSel(CBioseqContext &ctx)

void s_SetSelection(SAnnotSelector &sel, CBioseqContext &ctx)

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.

NCBI_DEPRECATED_CLASS NCBI_XCGI_EXPORT EUrlEncode encode

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

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 const char * GetErrCodeString(void) const

Get error code interpreted as text.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

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.

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

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

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

string GetLabel(const CSeq_id &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

void SetPacked_int(TPacked_int &v)

ENa_strand GetStrand(void) const

Get the location's strand.

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

Override Assign() to incorporate cache invalidation.

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CConstRef< CSeq_loc > GetRangeAsSeq_loc(void) const

Get seq-loc for the current iterator position.

CRef< CSeq_loc > Merge(TOpFlags flags, ISynonymMapper *syn_mapper) const

All functions create and return a new seq-loc object.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

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

bool IsEmpty(void) const

True if the current location is empty.

const CSeq_id * GetId(void) const

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

void SetPartialStart(bool val, ESeqLocExtremes ext)

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

ENa_strand GetStrand(void) const

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 SetPartialStop(bool val, ESeqLocExtremes ext)

void SetNull(void)

Override all setters to incorporate cache invalidation.

TSeqPos GetStop(ESeqLocExtremes ext) const

@ eOrder_Biological

Iterate sub-locations in positional order.

@ eEmpty_Allow

ignore empty locations

CMappedFeat GetBestGeneForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

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

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

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

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

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

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

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

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

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

Returns the sequence::ECompare containment relationship between CSeq_locs.

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

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

Merge ranges in the seq-loc.

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

Add two seq-locs.

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.

@ fCompareOverlapping

Check if seq-locs are overlapping.

@ eOverlap_SubsetRev

1st is a subset of 2nd ranges

@ eOverlap_Simple

any overlap of extremes

@ eContains

First CSeq_loc contains second.

@ eSame

CSeq_locs contain each other.

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

Get the encoding CDS feature of a given protein sequence.

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

Retrieve the Bioseq Handle from a location.

CConstRef< CSeq_feat > GetSourceFeatForProduct(const CBioseq_Handle &bsh)

vector< string > gap_linkage_evidences

A vector representing the linkage-evidences of the gap.

string gap_type

String representing the gap type.

CMappedFeat GetMappedmRNAForProduct(const CBioseq_Handle &product)

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

Given a CSeq_gap object, this outputs the Gap information.

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

Get bioseq handle for sequence withing one TSE.

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CSeq_loc_Mapper_Base & TruncateNonmappingRanges(void)

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

Add bioseq, return bioseq handle.

void RemoveBioseq(const CBioseq_Handle &seq)

Revoke Bioseq previously added using AddBioseq().

TCDD_Entries GetCDDAnnots(const TIds &idhs)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TBioseqHandles GetBioseqHandles(const TIds &ids)

Get bioseq handles for all ids.

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

vector< CBioseq_Handle > TBioseqHandles

CSeq_annot_Handle AddSeq_annot(CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add Seq-annot, return its CSeq_annot_Handle.

vector< CTSE_Handle > TCDD_Entries

Get CDD annotations for all ids.

vector< CSeq_id_Handle > TIds

void SetFuzzOption(TFuzzOption newOption)

@ fFuzzOption_RemoveLimTlOrTr

@ eProductToLocation

Map from the feature's product to location.

@ eLocationToProduct

Map from the feature's location to product.

vector< CSeq_id_Handle > TId

bool IsSetComment(void) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

const TInst_Hist & GetInst_Hist(void) const

TClass GetClass(void) const

const TInst_Ext & GetInst_Ext(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

CBioseq_set_Handle GetParentBioseq_set(void) const

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

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

bool CanGetClass(void) const

CConstRef< CSeq_id > GetInitialSeqIdOrNull(void) const

Get id used to obtain this bioseq handle.

bool IsSetInst_Hist(void) const

bool IsSetInst_Ext(void) const

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

bool IsSetProduct(void) const

virtual const CSeq_loc & GetLocation(void) const

TInst_Topology GetInst_Topology(void) const

const string & GetComment(void) const

const CSeq_annot::TDesc & Seq_annot_GetDesc(void) const

bool Seq_annot_CanGetDesc(void) const

bool IsSetInst(void) const

bool IsSetInst_Repr(void) const

bool IsTableSNP(void) const

Check if this is SNP table feature.

bool CanGetInst_Topology(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

TInst_Repr GetInst_Repr(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

bool CanGetId(void) const

CSeq_entry_Handle GetExactComplexityLevel(CBioseq_set::EClass cls) const

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

CSeqFeatData::ESubtype GetFeatSubtype(void) const

const CSeqMap & GetSeqMap(void) const

Get sequence map.

const string & GetName(void) const

bool IsPlainFeat(void) const

Check if this is plain feature.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

const TId & GetId(void) const

CConstRef< CBioseq_set > GetBioseq_setCore(void) const

Return core data for the bioseq-set.

bool Seq_annot_IsSetDesc(void) const

bool IsSynonym(const CSeq_id &id) const

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

const TInst & GetInst(void) const

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

SSeqMapSelector & SetResolveCount(size_t res_cnt)

Set max depth of resolving seq-map.

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)

SAnnotSelector & ExcludeFeatSubtype(TFeatSubtype subtype)

Exclude feature subtype from the search.

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & ExcludeFeatType(TFeatType type)

Exclude feature type from the search.

SAnnotSelector & SetResolveMethod(EResolveMethod resolve_method)

SetResolveMethod() controls visibility of subsegments depending on whether it's packaged together wit...

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 & ExcludeTSE(const CTSE_Handle &tse)

const CSeq_data & GetData(void) const

will allow only regular data segments (whole, plus strand)

SSeqMapSelector & SetFlags(TFlags flags)

Select segment type(s)

SAnnotSelector & SetOverlapType(EOverlapType overlap_type)

Set overlap type.

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetLimitNone(void)

Remove restrictions on the parent object of annotations.

SAnnotSelector & SetAdaptiveDepth(bool value=true)

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

SAnnotSelector & SetNoMapping(bool value=true)

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

SAnnotSelector & SetFeatComparator(IFeatComparator *comparator)

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

const CSeq_loc & GetProduct(void) const

bool IsSetData(void) const

SSeqMapSelector & SetLimitTSE(const CSeq_entry_Handle &tse)

Limit TSE to resolve references.

CSeq_id_Handle GetRefSeqid(void) const

The following function makes sense only when the segment is a reference to another seq.

bool IsUnknownLength(void) const

return true if current segment is a gap of unknown length

SAnnotSelector & SetOverlapIntervals(void)

Check overlapping of individual intervals.

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 & SetLimitTSE(const CTSE_Handle &limit)

Limit annotations to those from the TSE only.

SAnnotSelector & SetIgnoreStrand(bool value=true)

Ignore strand when testing for range overlap.

SAnnotSelector & SetSortOrder(ESortOrder sort_order)

Set sort order of annotations.

TSeqPos GetPosition(void) const

return position of current segment in sequence

TSeqPos GetLength(void) const

return length of current segment

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

@ eSortOrder_Reverse

decresing end, decreasing length

@ eSortOrder_Normal

default - increasing start, decreasing length

@ eOverlap_Intervals

default - overlapping of individual intervals

@ eResolve_TSE

default - search only on segments in the same TSE

CSeqMap_CI BeginResolved(CScope *scope) const

static CRef< CSeqMap > CreateSeqMapForSeq_loc(const CSeq_loc &loc, CScope *scope)

@ eSeqRef

reference to Bioseq

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

bool IsNull(void) const THROWS_NONE

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

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

bool IsNull(void) const THROWS_NONE

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

bool NotEmpty(void) const THROWS_NONE

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

TObjectType * GetNonNullPointer(void) const

Get pointer value and throw a null pointer exception if pointer is null.

bool Empty(void) const THROWS_NONE

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

position_type GetToOpen(void) const

#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.

virtual bool IsCanceled(void) const =0

static string HtmlDecode(const CTempString str, EEncoding encoding=eEncoding_Unknown, THtmlDecode *result_flags=NULL)

Decode HTML entities and character references.

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

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

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

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

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

Convert int to string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool 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.

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

Test for equality of a substring with another string.

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

Truncate whitespace in a string.

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

Case-sensitive compare of a substring with another string.

@ eNocase

Case insensitive compare.

#define DEFINE_STATIC_MUTEX(id)

Define static mutex and initialize it.

const TKeywords & GetKeywords(void) const

Get the Keywords member data.

const TSource & GetSource(void) const

Get the Source member data.

bool CanGetSource(void) const

Check if it is safe to call GetSource method.

bool CanGetKeywords(void) const

Check if it is safe to call GetKeywords method.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

bool IsSetOrg(void) const

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

bool CanGetOrg(void) const

Check if it is safe to call GetOrg method.

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.

TSubtype GetSubtype(void) const

Get the Subtype member data.

bool CanGetName(void) const

Check if it is safe to call GetName method.

void SetOrg(TOrg &value)

Assign a value to Org data member.

bool CanGetSubtype(void) const

Check if it is safe to call GetSubtype method.

const TName & GetName(void) const

Get the Name member data.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

bool IsStr(void) const

Check if variant Str is selected.

bool IsLim(void) const

Check if variant Lim is selected.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

TLim GetLim(void) const

Get the variant data.

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.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant 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.

@ eLim_circle

artificial break at origin of circle

const TMod & GetMod(void) const

Get the Mod member data.

bool CanGetMod(void) const

Check if it is safe to call GetMod method.

vector< CRef< CDbtag > > TDb

const TDb & GetDb(void) const

Get the Db member data.

list< CRef< COrgMod > > TMod

bool CanGetOrgname(void) const

Check if it is safe to call GetOrgname method.

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

list< CRef< CPub > > Tdata

const Tdata & Get(void) const

Get the member data.

@ e_Gen

general or generic unparsed

@ e_Proc

proceedings of a meeting

@ e_Man

manuscript, thesis, or letter

bool IsSetComment(void) const

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

const TPub & GetPub(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TRegion & GetRegion(void) const

Get the variant data.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

bool IsPub(void) const

Check if variant Pub is selected.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TProduct & GetProduct(void) const

Get the Product member data.

const TComment & GetComment(void) const

Get the Comment member data.

bool CanGetFrame(void) const

Check if it is safe to call GetFrame method.

TSite GetSite(void) const

Get the variant data.

void ResetLocation(void)

Reset Location data member.

bool IsSite(void) const

Check if variant Site is selected.

bool IsRna(void) const

Check if variant Rna is selected.

bool IsRegion(void) const

Check if variant Region is selected.

@ e_Het

cofactor, prosthetic grp, etc, bound to seq

@ e_Region

named region (globin locus)

@ e_Pub

publication applies to this seq

@ e_Comment

just a comment

@ eFrame_not_set

not set, code uses one

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetTo(TTo value)

Assign a value to To data member.

const TFuzz_from & GetFuzz_from(void) const

Get the Fuzz_from member data.

void ResetFuzz_to(void)

Reset Fuzz_to data member.

bool IsMix(void) const

Check if variant Mix is selected.

bool CanGetFuzz_to(void) const

Check if it is safe to call GetFuzz_to method.

list< CRef< CSeq_interval > > Tdata

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

const TId & GetId(void) const

Get the Id member data.

const TFuzz_to & GetFuzz_to(void) const

Get the Fuzz_to member data.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CSeq_loc > > Tdata

E_Choice Which(void) const

Which variant is currently selected.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSet(void) const

Check if a value has been assigned to data member.

void SetFrom(TFrom value)

Assign a value to From data member.

const Tdata & Get(void) const

Get the member data.

void ResetFuzz_from(void)

Reset Fuzz_from data member.

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.

bool IsSetTo(void) const

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

bool IsSetFuzz_to(void) const

Check if a value has been assigned to Fuzz_to 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 IsSetFrom(void) const

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

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsNull(void) const

Check if variant Null is selected.

bool IsSetFuzz_from(void) const

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

void SetStrand(TStrand value)

Assign a value to Strand data member.

E_Choice

Choice variants.

const TMix & GetMix(void) const

Get the variant data.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

const TAccession & GetAccession(void) const

Get the Accession member data.

bool CanGetFuzz_from(void) const

Check if it is safe to call GetFuzz_from method.

@ e_Gibbmt

Geninfo backbone moltype.

@ e_Giim

Geninfo import id.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_Gpipe

Internal NCBI genome pipeline processing ID.

@ e_Tpe

Third Party Annot/Seq EMBL.

@ e_Tpd

Third Party Annot/Seq DDBJ.

@ e_Gibbsq

Geninfo backbone seqid.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

@ e_not_set

No variant selected.

@ e_Tpg

Third Party Annot/Seq Genbank.

@ e_not_set

No variant selected.

bool CanGetSeq_set(void) const

Check if it is safe to call GetSeq_set method.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

@ eClass_parts

parts for 2 or 3

@ eClass_segset

segmented sequence + parts

void SetData(TData &value)

Assign a value to Data data member.

const Tdata & Get(void) const

Get the member data.

const TUser & GetUser(void) const

Get the variant data.

ERepr

representation class

TPub & SetPub(void)

Select the variant.

const TGap & GetGap(void) const

Get the variant data.

const TComment & GetComment(void) const

Get the Comment member data.

const TSource & GetSource(void) const

Get the variant data.

const TLiteral & GetLiteral(void) const

Get the variant data.

TTech GetTech(void) const

Get the Tech member data.

bool CanGetReplaced_by(void) const

Check if it is safe to call GetReplaced_by method.

bool IsSetReplaces(void) const

seq makes these seqs obsolete Check if a value has been assigned to Replaces data member.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

const TGenbank & GetGenbank(void) const

Get the variant data.

bool IsComment(void) const

Check if variant Comment is selected.

list< CRef< CSeq_id > > TIds

bool CanGetLength(void) const

Check if it is safe to call GetLength method.

bool IsDelta(void) const

Check if variant Delta is selected.

bool IsSet(void) const

Check if a value has been assigned to data member.

TSource & SetSource(void)

Select the variant.

E_Choice

Choice variants.

bool IsPub(void) const

Check if variant Pub is selected.

const TDelta & GetDelta(void) const

Get the variant data.

bool CanGetComment(void) const

Check if it is safe to call GetComment method.

TCompleteness GetCompleteness(void) const

Get the Completeness member data.

bool CanGetSeq_data(void) const

Check if it is safe to call GetSeq_data method.

const Tdata & Get(void) const

Get the member data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsLiteral(void) const

Check if variant Literal is selected.

list< CRef< CDelta_seq > > Tdata

const TReplaces & GetReplaces(void) const

Get the Replaces member data.

bool IsGap(void) const

Check if variant Gap is selected.

const TComment & GetComment(void) const

Get the variant data.

const TPub & GetPub(void) const

Get the Pub member data.

const TReplaced_by & GetReplaced_by(void) const

Get the Replaced_by member data.

list< CRef< CAnnotdesc > > Tdata

bool IsUser(void) const

Check if variant User is selected.

@ eRepr_seg

segmented sequence

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ eRepr_virtual

no seq data

@ eTech_htgs_2

ordered High Throughput sequence contig

@ eTech_targeted

targeted locus sets/studies

@ eTech_htgs_1

unordered High Throughput sequence contig

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_wgs

whole genome shotgun sequencing

@ eTech_htgs_0

single genomic reads for coordination

@ eBiomol_transcribed_RNA

transcribed RNA other than existing classes

@ e_User

user defined object

@ e_Pub

a reference to the publication

@ e_Genbank

GenBank specific info.

@ e_Comment

a more extensive comment

@ e_Region

overall region (globin locus)

@ e_Molinfo

info on the molecule and techniques

@ e_Maploc

map location of this sequence

@ e_Pdb

PDB specific information.

@ e_Name

a name for this sequence

@ e_Source

source of materials, includes Org-ref

bm::gap_word_t gap_length(const bm::gap_word_t *buf) noexcept

Returs GAP block length.

unsigned int

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

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

constexpr auto sort(_Init &&init)

const struct ncbi::grid::netcache::search::fields::SIZE size

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

Int4 delta(size_t dimension_, const Int4 *score_)

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

void AddPeriod(string &str)

const string & GetTechString(int tech)

EResolveOrder GetResolveOrder(CScope &scope, const CSeq_id_Handle &mrna, const CSeq_id_Handle &prot, CBioseq_Handle &mrna_bsh, CBioseq_Handle &prot_bsh)

bool GetModelEvidance(const CBioseq_Handle &bsh, SModelEvidance &me)

#define FOR_EACH_COMPOUND_ON_PDBBLOCK(Itr, Var)

FOR_EACH_COMPOUND_ON_PDBBLOCK EDIT_EACH_COMPOUND_ON_PDBBLOCK.

#define FIELD_IS_SET_AND_IS(Var, Fld, Chs)

FIELD_IS_SET_AND_IS base macro.

#define RAW_FIELD_IS_EMPTY_OR_UNSET(Var, Fld)

RAW_FIELD_IS_EMPTY_OR_UNSET macro.

#define STRING_FIELD_MATCH(Var, Fld, Str)

STRING_FIELD_MATCH base macro.

#define FIELD_CHOICE_EQUALS(Var, Fld, Chs, Value)

FIELD_CHOICE_EQUALS base macro.

#define STRING_FIELD_CHOICE_MATCH(Var, Fld, Chs, Value)

STRING_FIELD_CHOICE_MATCH base macro.

static SLJIT_INLINE sljit_ins sgr(sljit_gpr dst, sljit_gpr src)

#define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array)

This indicates the text of the modifiers of a gap.

vector< string > gap_evidence

Selector used in CSeqMap methods returning iterators.

bool operator()(const CRef< CSourceFeatureItem > &sfp1, const CRef< CSourceFeatureItem > &sfp2)

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

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