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

m_MappedObject.Reset();

m_MappedObjectType = eMappedObjType_not_set;

vector<CHandleRangeMap> hrmaps;

( vector<CHandleRangeMap>, rowit, hrmaps ) {

( dst_ids.

(idit->first) != dst_ids.

() ) {

range.

(idit->second.GetOverlappingRange());

interval.

(

);

.GetFeatFast()->GetProduct() :

.GetFeatFast()->GetLocation();

rg = it.GetRange();

& ext = (*m_Map)[it.GetSeq_id_Handle()];

( !ext.

() ) {

&

(*m_MappedObject);

: m_Seq_annot(annot_handle),

m_AnnotIndex(object.GetAnnotIndex()),

m_AnnotType(eAnnot_Regular)

(

.

() ) {

(

.IsRegular() ) {

& feat = *

.GetFeatFast();

(

.HasSingleKey() ) {

beg =

.GetKeysBegin();

end =

.GetKeysEnd();

: m_Seq_annot(annot_handle),

m_AnnotIndex(

(snp_annot.GetIndex(snp))),

m_AnnotType(eAnnot_SNPTable)

( src_from == src_to ) {

: m_Seq_annot(annot_handle),

m_AnnotType(eAnnot_SortedSeqTable)

(

.

() ) {

& feat = *

.GetFeatFast();

( !

.IsMapped() ) {

(

.GetMappedObjectType() ==

.eMappedObjType_Seq_feat ) {

.GetMappedSeq_feat();

.SetMappedSeq_feat(*mapped_feat);

.GetMappedSeq_feat();

*

variation_key =

;

variation_key;

(

.IsMappedLocation() ) {

(

.GetMappedObjectType() ==

.eMappedObjType_Seq_feat ) {

(

.GetMappedObjectType() ==

.eMappedObjType_Seq_loc ) {

.GetMappedSeq_loc().GetStrand();

.GetMappedStrand();

.GetMappedStrand();

(

.IsMappedLocation() ) {

(

.GetMappedObjectType() ==

.eMappedObjType_Seq_loc ) {

(

.GetMappedObjectType() ==

.eMappedObjType_Seq_id ) {

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

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

+= (**it).GetVal();

( !

.empty()) {

( x_annot_type != y_annot_type ) {

x_annot_type < y_annot_type;

x_feat_type =

.GetFeatType();

x_feat_subtype =

.GetFeatSubtype();

y_feat_type =

.GetFeatType();

y_feat_subtype =

.GetFeatSubtype();

( x_feat_subtype != y_feat_subtype ) {

x_order =

(x_feat_type, x_feat_subtype);

y_order =

(y_feat_type, y_feat_subtype);

( x_order != y_order ) {

x_order < y_order;

( x_minus != y_minus ) {

( x_complex != y_complex ) {

x_minus ^ y_complex;

( x_feat_subtype != y_feat_subtype ) {

x_feat_subtype < y_feat_subtype;

(x_feat_type == y_feat_type);

( x_frame != y_frame ) {

x_frame < y_frame;

* x_key = x_create.

();

* y_key = y_create.

();

( x_key != y_key ) {

( x_has_product != y_has_product ) {

!x_has_product;

( x_has_product ) {

( x_has_label != y_has_label ) {

!x_has_label;

( x_has_label ) {

all_minus =

;

all_non_minus =

;

( ; loc_ci; ++loc_ci ) {

( ! first_piece ) {

first_piece = loc_ci;

last_piece = loc_ci;

all_non_minus =

;

lowest = piece_start;

lowest =

( lowest, piece_start );

highest = piece_stop;

highest =

( highest, piece_stop );

( ! all_minus && ! all_non_minus ) {

is_circular =

;

( first_piece ) {

( first_piece ) {

x_circular = x_from >= x_to;

y_circular = y_from >= y_to;

( x_circular != y_circular ) {

x_circular ? -1 : 1;

( x_from != y_from ) {

x_from < y_from ? -1 : 1;

( x_to != y_to ) {

x_to > y_to ? -1 : 1;

(; x_it != x_idmap.

() && y_it != y_idmap.

(); ++x_it, ++y_it) {

(x_it->first != y_it->first)

x_it->first < y_it->first;

=

(x_it->second.from, x_it->second.to, y_it->second.from, y_it->second.to);

(

!= 0)

< 0;

(y_it != y_idmap.

())

;

(x_it != x_idmap.

())

;

x_circular = x_from >= x_to;

y_circular = y_from >= y_to;

( x_circular != y_circular ) {

( x_from != y_from ) {

x_from < y_from;

( x_to != y_to ) {

(; x_it != x_idmap.

() && y_it != y_idmap.

(); ++x_it, ++y_it) {

(x_it->first != y_it->first)

y_it->first < x_it->first;

x_it->second.from, x_it->second.to, y_it->second.from, y_it->second.to);

(

!= 0)

> 0;

(x_it != x_idmap.

())

;

(y_it != y_idmap.

())

;

x_circular = x_from >= x_to;

y_circular = y_from >= y_to;

( x_circular != y_circular ) {

( x_to != y_to ) {

( x_from != y_from ) {

x_from < y_from;

(&orig_feat, 0, &created_point, &created_interval);

(&orig_feat, 0, &created_point, &created_interval);

(

.MappedSeq_locNeedsUpdate() ) {

( mapped_feat ) {

mapped_feat.

();

(0, &mapped_loc, &created_point, &created_interval);

.UpdateMappedSeq_loc(mapped_loc,

(0, &mapped_loc, &created_point, &created_interval);

(

.IsMapped() ) {

ret =

*

(&

.GetMappedSeq_loc());

( !

.IsMapped() ) {

( !

.MappedSeq_locNeedsUpdate() ) {

(

*

(&

.GetMappedSeq_loc()));

(

.GetMappedObjectType() ==

.eMappedObjType_Seq_feat) {

(

.GetMappedObjectType() ==

.eMappedObjType_Seq_feat) {

ret = &

.GetMappedSeq_feat();

( !

.IsMapped() ) {

.InitializeMappedSeq_feat(orig_feat, *mapped_feat);

( !

.IsMappedLocation() ) {

( !

.IsMappedProduct() ) {

(

.IsMappedLocation() ) {

(

.IsMappedProduct() ) {

(

.IsPartial() ) {

m_FromOtherTSE(

)

>= limit;

=

(

=

- 1;

>= 0; --

) {

pair<size_t, size_t> idxs =

(

= idxs.first;

< idxs.second; ++

) {

pair<size_t, size_t> range =

(

index = range.first; index < range.second; ++index ) {

( max_time <= 86400 ) {

( !

.IsNamed() ) {

found_accs.

(acc);

( !found_accs.

() ) {

(

& acc : found_accs ) {

);

master_range.

(range, strand);

exact_depth = selector.

() && depth_is_set;

deeper =

;

( adaptive_flags || !exact_depth ||

== 0 ) {

deeper =

> 0 &&

( deeper && by_policy ) {

only_named_annot_accs =

;

unique_ptr<SAnnotSelector> local_sel;

( deeper && adaptive_flags ) {

(

level = 1; level <=

&& deeper; ++level ) {

( adaptive_flags || !exact_depth ||

== level ) {

*master_loc_empty, level);

deeper =

> level;

( deeper && adaptive_flags ) {

(

<<

(

level = 1; level <= last_depth; ++level ) {

( adaptive_flags || !exact_depth ||

== level ) {

*master_loc_empty, level, cvt_set);

exact_depth = selector.

() && depth_is_set;

deeper =

;

( adaptive_flags || !exact_depth ||

== 0 ) {

deeper =

> 0 &&

( deeper && adaptive_flags ) {

(

level = 1; level <=

&& deeper; ++level ) {

( adaptive_flags || !exact_depth ||

== level ) {

deeper =

> level;

( deeper && adaptive_flags ) {

(

<<

(

level = 1; level <= last_depth; ++level ) {

( adaptive_flags || !exact_depth ||

== level ) {

master_range, 0, check_adaptive);

( !only_gi || syn_it->IsGi() ) {

master_range, 0, check_adaptive);

master_range, 0, check_adaptive);

syns_initialized =

;

& tse_info = *tse_it->first;

( !syns_initialized ) {

syns_initialized =

;

master_range, 0, check_adaptive);

syns->GetSeq_id_Handle(syn_it),

master_range, 0, check_adaptive);

( !only_gi || syn_it->IsGi() ) {

master_range, 0, check_adaptive);

has_more =

;

(smit, master_loc_empty, master_id, master_range);

top_level)

);

&

(*idit->first.GetSeqId()));

has_more =

;

);

&

(*idit->first.GetSeqId()));

(smit, *master_loc_empty, idit->first, idit->second);

(iter->second == tse);

&

.x_GetInfo() < &

.x_GetInfo();

&

.x_GetInfo() <

;

< &

.x_GetInfo();

loc_index)

vector<CAnnotObject_Ref> partial_refs;

( !amit->second ) {

amit->second->Convert(annot_ref, loctype);

( amit->second->IsPartial() &&

amit->second->HasUnconvertedId() ) {

feat.

(*

, obj);

graph.

(*

, obj);

amit->second.GetNCObject().Convert(annot_ref, loctype);

(

<<

cvt.

(annot_ref, loctype);

(

<<

it->GetMappingInfo().SetIdRangeMap(*id_rg_map);

== limit;

(

== limit ) {

( !

->HasParent_Info() ) {

= &

->GetParentSeq_entry_Info();

== limit;

);

);

check_adaptive)

(tseh,

, hr, cvt, check_adaptive);

check_adaptive)

found =

;

( check_adaptive &&

index <

; ++index ) {

index <

; ++index ) {

loc_index)

( !mapping_set ) {

mapping_set->

(*cvt_copy, loc_index);

(tseh, objs, guard, annot_name,

, hr, cvt);

kAnnotTypeIndex_SNP =

( snp_it != snp_annot.

() ) {

( !sah || &sah.

() != &annot_info ) {

sah.

(annot_info, tseh);

( snp.

(range) ) {

}

( ++snp_it != snp_annot.

() );

( xrefs.size() == 1 ) {

(

.IsGene() ) {

from_idx = 0;

enough =

;

vector<const CTSE_Chunk_Info*> TStubs;

restart =

;

( TStubs, it, stubs ) {

(

& it : stubmap) {

it.first->LoadChunk(it.second.front());

it.second.erase(unique(it.second.begin(), it.second.end()), it.second.end());

it.first->LoadChunks(it.second);

index <

; ++index ) {

need_unique =

;

aoit(rmap.

(range));

*aoit->second.m_AnnotObject_Info;

annot_info.

() ) {

stubs.push_back(&chunk);

( annot_info.

() ) {

( !ref_loc.

() ) {

);

loc_from = aoit->first.GetFrom();

loc_to = aoit->first.GetTo();

ref_search_range.

(ref_from + (loc_view_from - loc_from),

ref_to + (loc_view_to - loc_to));

ref_search_range.

(ref_from - (loc_view_to - loc_to),

ref_to - (loc_view_from - loc_from));

ref_rmap.

(ref_idh).AddRange(ref_search_range,

( !

(hr, aoit->first, aoit->second) ) {

sah.

(seq_annot, tseh);

is_circular = aoit->second.m_HandleRange &&

aoit->second.m_HandleRange->GetData().IsCircular();

need_unique |= is_circular;

( !sah || &sah.

() != &sa_info ){

sah.

(sa_info, tseh);

( !cvt && aoit->second.GetMultiIdFlag() ) {

from = aoit->second.m_HandleRange->

GetData().GetLeft();

to =aoit->second.m_HandleRange->

GetData().GetRight();

aoit->second.m_AnnotLocationIndex);

(cvt && !annot_ref.

() ) {

( is_circular ) {

from = aoit->second.m_HandleRange->

GetData().GetLeft();

to = aoit->second.m_HandleRange->

GetData().GetRight();

aoit->second.m_AnnotLocationIndex);

( need_unique || hr.

() - hr.

() > 1 ) {

TAnnotSet::iterator first_added =

.begin() + start_size;

}

( restart );

found =

;

( idit->second.Empty() ) {

);

syns->GetSeq_id_Handle(syn_it),

idit->second, cvt, check_adaptive);

( !only_gi || syn_it->IsGi() ) {

idit->second, cvt, check_adaptive);

found |=

(tse_it->first, tse_it->second,

idit->second, cvt, check_adaptive);

& tse_info = *tse_it->first;

found |=

(tse_it->second, idit->first,

idit->second, cvt, check_adaptive);

syns_initialized =

;

& tse_info = *tse_it->first;

( !syns_initialized ) {

syns_initialized =

;

found |=

(tse_it->second, idit->first,

idit->second, cvt, check_adaptive);

syns->GetSeq_id_Handle(syn_it),

idit->second, cvt, check_adaptive);

( !only_gi || syn_it->IsGi() ) {

idit->second, cvt, check_adaptive);

);

( entry_info.

() ) {

kAnnotTypeIndex_SNP =

shift = ref_seg_range.

() - master_seg_range.

();

shift = ref_seg_range.

() + master_seg_range.

();

( !range.

() ) {

);

);

);

shift = ref_seg_range.

() - master_seg_range.

();

shift = ref_seg_range.

() + master_seg_range.

();

( !range.

() ) {

->insert(it->GetSeq_annot_Info().GetName());

static CRef< CScope > m_Scope

bool IsReverse(ENa_strand s)

ENa_strand Reverse(ENa_strand s)

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static bool sx_IsEmpty(const SAnnotSelector &sel)

static const bool kTraceFullCvt

NCBI_DEFINE_ERR_SUBCODE_X(2)

static bool sx_GeneIsSuppressed(const CSeq_feat &feat)

static CScope::EGetBioseqFlag sx_GetFlag(const SAnnotSelector &selector)

static CSeqFeatData::ESubtype s_DefaultAdaptiveTriggers[]

Annotation iterators exceptions.

map< CAnnotObject_Ref, CRef< CSeq_loc_Conversion_Set > > TAnnotMappingSet

TAnnotMappingSet m_AnnotMappingSet

void InitializeMappedSeq_feat(const CSeq_feat &src, CSeq_feat &dst) const

const CSeq_align & GetMappedSeq_align(const CSeq_align &orig) const

bool MappedSeq_locNeedsUpdate(void) const

void SetMappedSeq_align_Cvts(CSeq_loc_Conversion_Set &cvts)

CRef< CObject > m_MappedObject

const CIdRangeMap & GetIdRangeMap(void) const

void SetMappedSeq_id(CSeq_id &id)

void SetTotalRange(const TRange &range)

const CGraphRanges * GetGraphRanges(void) const

void SetGraphRanges(CGraphRanges *ranges)

const TRange & GetTotalRange(void) const

bool IsMappedLocation(void) const

void SetIdRangeMap(CIdRangeMap &id_range_map)

TSeqPos GetFrom(void) const

bool IsMapped(void) const

void UpdateMappedSeq_loc(CRef< CSeq_loc > &loc, CRef< CSeq_point > &pnt_ref, CRef< CSeq_interval > &int_ref, const CSeq_feat *orig_feat) const

EMappedObjectType GetMappedObjectType(void) const

ENa_strand GetMappedStrand(void) const

const CSeq_id * GetProductId(void) const

const CSeq_feat & GetMappedSeq_feat(void) const

TSeqPos GetToOpen(void) const

bool IsMappedProduct(void) const

const CSeq_id * GetLocationId(void) const

bool IsMappedPoint(void) const

@ eMappedObjType_IdRangeMap

@ eMappedObjType_Seq_align

@ eMappedObjType_Seq_loc_Conv

@ eMappedObjType_Seq_feat

@ eMappedObjType_Seq_loc_Conv_Set

void SetMappedConverstion(CSeq_loc_Conversion &cvt)

void SetMappedSeq_feat(CSeq_feat &feat)

void SetMappedStrand(ENa_strand strand)

bool IsPartial(void) const

void SetPartial(bool value)

void SetMappedSeq_align(CSeq_align *align)

CRef< CGraphRanges > m_GraphRanges

const CSeq_id & GetMappedSeq_id(void) const

CSeq_loc_Conversion & GetMappedSeq_loc_Conv(void) const

void SetAnnotObjectRange(const TRange &range, bool product)

const CSeq_loc & GetMappedSeq_loc(void) const

CBioseq_Handle m_BioseqHandle

CNearnessTester(const CBioseq_Handle &handle)

bool operator()(const CSeq_id *id) const

DECLARE_OPERATOR_BOOL(m_BioseqHandle)

const CTSE_Chunk_Info & GetChunk_Info(void) const

const CSeq_loc & GetLocs(void) const

const CSeq_annot_Info & GetSeq_annot_Info(void) const

const CSeq_graph & GetGraph(void) const

bool IsRegular(void) const

static void x_ProcessAlign(vector< CHandleRangeMap > &hrmaps, const CSeq_align &align, const CMasterSeqSegments *master)

const CSeq_feat * GetFeatFast(void) const

TFeatSubtype GetFeatSubtype(void) const

TIndex GetAnnotIndex(void) const

const CSeq_feat & GetFeat(void) const

TFeatType GetFeatType(void) const

bool IsChunkStub(void) const

TAnnotType GetAnnotType(void) const

const CSeq_align & GetAlign(void) const

bool IsRemoved(void) const

const CSeq_annot_SNP_Info & GetSeq_annot_SNP_Info(void) const

bool IsSortedSeqTableFeat(void) const

const CSeq_graph & GetGraph(void) const

const CAnnotObject_Info & GetAnnotObject_Info(void) const

bool IsAnySeqTableFeat(void) const

const SSNP_Info & GetSNP_Info(void) const

const CSeq_annot_Info & GetSeq_annot_Info(void) const

bool IsSNPTableFeat(void) const

const CSeq_align & GetAlign(void) const

const CSeq_feat & GetFeat(void) const

bool IsFromOtherTSE(void) const

CAnnotMapping_Info m_MappingInfo

void SetFromOtherTSE(bool from_other_tse=true)

TAnnotIndex GetAnnotIndex(void) const

bool IsPlainFeat(void) const

const CSeqTableInfo & GetSeqTableInfo(void) const

bool HasAnnotObject_Info(void) const

CAnnotMapping_Info & GetMappingInfo(void) const

static size_t GetSubtypeIndex(CSeqFeatData::ESubtype subtype)

static SAnnotTypeSelector GetTypeSelector(size_t index)

static TIndexRange GetIndexRange(const SAnnotTypeSelector &sel)

TMaxSearchSegments m_SearchSegments

unique_ptr< TAnnotLocsSet > m_AnnotLocsSet

void x_Initialize0(const SAnnotSelector &selector)

void x_SearchObjects(const CTSE_Handle &tse, const SIdAnnotObjs *objs, CMutexGuard &guard, const CAnnotName &name, const CSeq_id_Handle &id, const CHandleRange &hr, CSeq_loc_Conversion *cvt)

bool x_FoundAllNamedAnnotAccessions(unique_ptr< SAnnotSelector > &local_sel)

bool x_SearchTSE2(const CTSE_Handle &tse, const CSeq_id_Handle &id, const CHandleRange &hr, CSeq_loc_Conversion *cvt, bool check_adaptive)

CAnnot_Collector(CScope &scope)

TTSE_LockMap m_TSE_LockMap

vector< SAnnotTypeSelector > TAnnotTypes

void x_AddObject(CAnnotObject_Ref &object_ref)

const TAnnotTypes & x_GetAnnotTypes(void) const

unique_ptr< CAnnotMappingCollector > m_MappingCollector

bool x_SearchSegments(const CBioseq_Handle &bh, const CSeq_id_Handle &master_id, const CHandleRange &master_range, CSeq_loc &master_loc_empty, int level)

void x_SearchMaster(const CBioseq_Handle &bh, const CSeq_id_Handle &master_id, const CHandleRange &master_range)

void x_AddPostMappings(void)

bool x_CheckAdaptive(const CSeq_id_Handle &id) const

void x_StopSearchLimits(void)

void x_AddPostMappingsCvt(CSeq_loc_Conversion_Set &cvt)

bool x_SearchMapped(const CSeqMap_CI &seg, CSeq_loc &master_loc_empty, const CSeq_id_Handle &master_id, const CHandleRange &master_hr)

CBioseq_Handle x_GetBioseqHandle(const CSeq_id_Handle &id, bool top_level=false) const

bool x_MaxSearchSegmentsLimitIsReached(void) const

bool x_MatchLocIndex(const SAnnotObject_Index &index) const

void x_CollectSegments(const CBioseq_Handle &bh, const CSeq_id_Handle &master_id, const CHandleRange &master_range, CSeq_loc &master_loc_empty, int level, CSeq_loc_Conversion_Set &cvt_set)

bool x_SearchLoc(const CHandleRangeMap &loc, CSeq_loc_Conversion *cvt, const CTSE_Handle *using_tse, bool top_level=false)

set< CAnnotName > TAnnotNames

TAnnotTypesBitset m_CollectAnnotTypes

void x_AddTSE(const CTSE_Handle &tse)

bool CanResolveId(const CSeq_id_Handle &idh, const CBioseq_Handle &bh)

SAnnotSelector::EMaxSearchSegmentsAction m_SearchSegmentsAction

bool x_MatchRange(const CHandleRange &hr, const CRange< TSeqPos > &range, const SAnnotObject_Index &index) const

bool x_MatchLimitObject(const CAnnotObject_Info &annot_info) const

vector< CAnnotObject_Ref > TAnnotSet

bool x_NoMoreObjects(void) const

TAnnotTypesBitset m_TriggerTypes

const TAnnotNames & x_GetAnnotNames(void) const

void x_Initialize(const SAnnotSelector &selector, const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand)

TAnnotTypes m_AnnotTypes2

double x_GetCostOfLoadingInSeconds(void) const

TAnnotTypesBitset m_UnseenAnnotTypes

CConstRef< CSerialObject > x_GetMappedObject(const CAnnotObject_Ref &obj)

Uint8 x_GetCostOfLoadingInBytes(void) const

void x_SearchRange(const CTSE_Handle &tse, const SIdAnnotObjs *objs, CMutexGuard &guard, const CAnnotName &name, const CSeq_id_Handle &id, const CHandleRange &hr, CSeq_loc_Conversion *cvt)

void x_AddObjectMapping(CAnnotObject_Ref &object_ref, CSeq_loc_Conversion *cvt, unsigned int loc_index)

SAnnotSelector::TMaxSize TMaxSize

void x_CollectMapped(const CSeqMap_CI &seg, CSeq_loc &master_loc_empty, const CSeq_id_Handle &master_id, const CHandleRange &master_hr, CSeq_loc_Conversion_Set &cvt_set)

TAnnotTypesBitset m_AnnotTypes

const SAnnotSelector * m_Selector

bool x_SearchTSE(const CTSE_Handle &tse, const CSeq_id_Handle &id, const CHandleRange &hr, CSeq_loc_Conversion *cvt, bool check_adaptive)

const SAnnotSelector & GetSelector(void) const

unique_ptr< TAnnotNames > m_AnnotNames

const TAnnot & GetAnnot(void) const

vector< CRef< CSeq_annot_Info > > TAnnot

vector< CRef< CSeq_entry_Info > > TSeq_set

const CSeq_feat & GetOriginalFeat(void)

ENa_strand GetStrand(bool by_product)

const CSeq_loc * GetComplexLoc(bool by_product)

const CAnnotObject_Ref & m_Ref

const CSeq_feat & GetMappedFeat(void)

int GetCdregionOrder(void)

const char * GetImpKey(void)

string GetFeatLabel(void)

CRef< CSeq_feat > m_CreatedOriginalFeat

static const CSeq_loc & GetLoc(const CSeq_feat &feat, bool by_product)

CConstRef< CSeq_id > GetProductId(void)

CCreateFeat(const CAnnotObject_Ref &ref, const CAnnotObject_Info *info)

const CAnnotObject_Info * m_Info

CConstRef< CSeq_feat > GetOriginalFeature(const CSeq_feat_Handle &feat_h)

CRef< CSeq_loc > m_CreatedSeq_loc

CRef< CSeq_loc > GetMappedLocation(const CAnnotMapping_Info &map, const CSeq_feat &orig_feat)

CRef< CSeq_point > m_CreatedSeq_point

CRef< CSeq_interval > m_CreatedSeq_interval

void ReleaseRefsTo(CRef< CSeq_feat > *feat, CRef< CSeq_loc > *loc, CRef< CSeq_point > *point, CRef< CSeq_interval > *interval)

CRef< CSeq_feat > m_CreatedSeq_feat

void ResetRefsFrom(CRef< CSeq_feat > *feat, CRef< CSeq_loc > *loc, CRef< CSeq_point > *point, CRef< CSeq_interval > *interval)

CConstRef< CSeq_feat > GetMappedFeature(const CAnnotMapping_Info &map, const CSeq_feat &orig_feat)

Helper class for mapping graphs.

void Guard(resource_type &resource)

Manually force the guard to protect some other resource.

void Release()

Manually force the resource to be released.

void AddRanges(const CSeq_id_Handle &h, const CHandleRange &hr)

const_iterator find(const CSeq_id_Handle &idh) const

const TLocMap & GetMap(void) const

TLocMap::const_iterator const_iterator

const_iterator end(void) const

TTotalRangeFlags GetStrandsFlag(void) const

void AddRange(TRange range, ENa_strand strand)

bool IntersectingWith(const CHandleRange &hr) const

const_iterator begin(void) const

bool IntersectingWithTotalRange(const CHandleRange &hr) const

bool IntersectingWith_NoStrand(const CHandleRange &hr) const

TRange GetOverlappingRange(TTotalRangeFlags flags=eStrandAny) const

const_iterator end(void) const

map< CSeq_id_Handle, SExtremes > TIdRangeMap

virtual ~CIdRangeMap(void)

unique_ptr< TIdRangeMap > m_Map

CIdRangeMap(const CAnnotObject_Ref &annot_ref, const SAnnotSelector &sel)

const TIdRangeMap & GetMap(void) const

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

vector< pair< CTSE_Handle, CSeq_id_Handle > > TTSE_LockMatchSet

CConstRef< CSynonymsSet > GetSynonyms(const CSeq_id_Handle &id, int get_flag)

CBioseq_Handle GetBioseqHandle(const CSeq_id_Handle &id, int get_flag)

TIds GetIds(const CSeq_id_Handle &idh, TGetFlags flags=0)

void GetTSESetWithAnnots(const CSeq_id_Handle &idh, TTSE_LockMatchSet &tse_set)

CConstRef< CSeq_id > GetLocationId(size_t row) const

void UpdateSeq_feat(size_t row, CRef< CSeq_feat > &seq_feat, CRef< CSeq_point > &seq_pnt, CRef< CSeq_interval > &seq_int) const

SAnnotTypeSelector GetType(void) const

ENa_strand GetLocationStrand(size_t row) const

const SAnnotObject_Key & GetAnnotObjectKey(size_t i) const

const TAnnotObjectInfos & GetAnnotObjectInfos(void) const

const CAnnotObject_Info & GetInfo(TAnnotIndex index) const

bool TableFeat_HasLabel(TAnnotIndex index) const

string TableFeat_GetLabel(TAnnotIndex index) const

bool MatchBitFilter(const SAnnotSelector &sel, const CSeq_annot_SortedIter &iter) const

bool IsSortedTable(void) const

const CAnnotName & GetName(void) const

bool x_HasSNP_annot_Info(void) const

SAnnotObjectsIndex::TObjectInfos TAnnotObjectInfos

void UpdateAnnotIndex(void) const

const CSeqTableInfo & GetTableInfo(void) const

static const TAnnotIndex kWholeAnnotIndex

CSeq_annot_SortedIter StartSortedIterator(CRange< TSeqPos > range) const

const CSeq_annot_SNP_Info & x_GetSNP_annot_Info(void) const

const CSeq_id & GetSeq_id(void) const

const SSNP_Info & GetInfo(size_t index) const

const CSeq_annot_Info & GetParentSeq_annot_Info(void) const

TSNP_Set::const_iterator const_iterator

const_iterator end(void) const

const_iterator FirstIn(const TRange &range) const

const CRange< TSeqPos > & GetRange(void) const

const CBioseq_Base_Info & x_GetBaseInfo(void) const

void UpdateAnnotIndex(void) const

const TSet & GetSet(void) const

namespace ncbi::objects::

int GetTypeSortingOrder(void) const

Return relative importance order of features by their type.

Used as a helper for determining which pieces of a CSeq_loc to compare.

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

void Add(CSeq_loc_Conversion &cvt, unsigned int loc_index)

const TSeq_id_Handles & GetDst_id_Handles(void) const

void Convert(CAnnotObject_Ref &obj, CSeq_loc_Conversion::ELocationType loctype)

bool Convert(const CSeq_loc &src, CRef< CSeq_loc > &dst, EConvertFlag flag=eCnvDefault)

bool IsPartial(void) const

void MakeDstMix(CSeq_loc_mix &dst, const CSeq_loc_mix &src) const

bool ConvertInterval(TSeqPos src_from, TSeqPos src_to, ENa_strand src_strand)

void SetMappedLocation(CAnnotObject_Ref &ref, ELocationType loctype)

const CSeq_id & GetId(void) const

void CombineWith(CSeq_loc_Conversion &cvt)

bool ConvertPoint(TSeqPos src_pos, ENa_strand src_strand)

void SetSrcId(const CSeq_id_Handle &src)

TChunkId GetChunkId(void) const

const CTSE_Split_Info & GetSplitInfo(void) const

pair< Uint4, double > GetLoadCost() const

bool NotLoaded(void) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from this TSE.

bool AddUsedTSE(const CTSE_Handle &tse) const

Register argument TSE as used by this TSE, so it will be released by scope only after this TSE is rel...

const CTSE_Info & x_GetTSE_Info(void) const

bool x_DirtyAnnotIndex(void) const

TNamedAnnotObjs m_NamedAnnotObjs

void UpdateAnnotIndex(const CSeq_id_Handle &id) const

bool OnlyGiAnnotIds(void) const

CSeq_id_Handle ContainsMatchingBioseq(const CSeq_id_Handle &id) const

SIdAnnotObjs::TSNPSet TSNPSet

bool HasMatchingAnnotIds(void) const

TAnnotLock & GetAnnotLock(void) const

const SIdAnnotObjs * x_GetIdObjects(const TAnnotObjs &objs, const CSeq_id_Handle &idh) const

const SIdAnnotObjs * x_GetUnnamedIdObjects(const CSeq_id_Handle &id) const

container_type::const_iterator const_iterator

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

iterator_bool insert(const value_type &val)

container_type::value_type value_type

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

parent_type::const_iterator const_iterator

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

static const struct name_t names[]

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.

int TSignedSeqPos

Type for signed sequence position.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define LOG_POST(message)

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

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

static const TObjectType * SafeCast(TTypeInfo type)

#define MSerial_AsnText

I/O stream manipulators –.

const string AsFastaString(void) const

CConstRef< CSeq_id > GetSeqId(void) const

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

ENa_strand GetStrand(void) const

Get the location's strand.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsSetStrand(void) const

Get strand.

CSeq_id_Handle GetSeq_id_Handle(void) const

int CompareSubLoc(const CSeq_loc &loc, ENa_strand strand, const ISubLocFilter *filter=NULL) const

Compare first-level sub-locations sequentially to order them by biological "complexity".

const CSeq_id * GetId(void) const

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

TRange GetRange(void) const

Get the range.

void InvalidateTotalRangeCache(void) const

ENa_strand GetStrand(void) const

void SetNull(void)

Override all setters to incorporate cache invalidation.

TSeqPos GetStop(ESeqLocExtremes ext) const

@ eOrder_Biological

Iterate sub-locations in positional order.

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,...

@ eGetBioseq_Loaded

Search in all loaded TSEs in the scope.

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

const CSeq_annot_SNP_Info & x_GetSNP_annot_Info(void) const

const SSNP_Info & x_GetSNP_Info(void) const

vector< CSeq_id_Handle > TId

TFeatIndex x_GetFeatIndex() const

EFeatureFetchPolicy GetFeatureFetchPolicy(void) const

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

void x_Set(const CSeq_annot_Info &annot, const CTSE_Handle &tse)

CSeq_id_Handle GetAccessSeq_id_Handle(void) const

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

CConstRef< CSeq_feat > m_CreatedOriginalFeat

TInst_Topology GetInst_Topology(void) const

bool IsTableSNP(void) const

Check if this is SNP table feature.

bool CanGetInst_Topology(void) const

const CSeq_annot_Info & x_GetSeq_annot_Info(void) const

const CSeq_annot_Info & x_GetInfo(void) const

CConstRef< CSeq_feat > GetPlainSeq_feat(void) const

Get current seq-feat.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

bool IsTableFeat(void) const

Check if this is non-SNP table feature.

const CSeqMap & GetSeqMap(void) const

Get sequence map.

const TId & GetId(void) const

bool IsSynonym(const CSeq_id &id) const

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

@ eFeatureFetchPolicy_default

@ eFeatureFetchPolicy_only_near

vector< SAnnotTypeSelector > TAdaptiveTriggers

TSeqPos GetEndPosition(void) const

return end position of current segment in sequence (exclusive)

AutoPtr< CHandleRangeMap > m_SourceLoc

bool m_CollectCostOfLoading

EResolveMethod m_ResolveMethod

bool GetExactDepth(void) const

GetExactDepth() returns current value of 'exact depth' flag.

vector< CAnnotName > TAnnotsNames

Object manager recognizes several fields of Seq-annot as annot name.

TMaxSearchTime GetMaxSearchTime(void) const

Get maximum time (in seconds) to search before giving up.

void Set(CAnnot_Collector &collector, const CAnnotObject_Ref &annot_ref)

SSeqMapSelector & SetBySequenceClass(void)

bool IsIncludedAnyNamedAnnotAccession(void) const

check if any named annot accession is included in the search

EUnresolvedFlag m_UnresolvedFlag

CConstRef< CObject > m_LimitObject

TSeqPos GetRefPosition(void) const

TMaxSearchSegments GetMaxSearchSegments(void) const

Get maximum number of empty segments to search before giving up.

void CheckLimitObjectType(void) const

EMaxSearchSegmentsAction GetMaxSearchSegmentsAction(void) const

int GetResolveDepth(void) const

GetResolveDepth() returns current limit of subsegment resolution in searching annotations.

ELimitObject m_LimitObjectType

EResolveMethod GetResolveMethod(void) const

GetResolveMethod() returns current value of resolve_method.

bool HasBitFilter(void) const

TAnnotTypesBitset m_AnnotTypesBitset

bool ExcludedAnnotName(const CAnnotName &name) const

TAdaptiveTriggers m_AdaptiveTriggers

TMaxSize GetMaxSize(void) const

Get maximum allowed number of annotations to find.

const CSeq_graph & GetMappedGraph(void) const

Graph mapped to the master sequence.

virtual bool Less(const CSeq_feat &f1, const CSeq_feat &f2, CScope *scope)=0

bool GetRefMinusStrand(void) const

TAdaptiveDepthFlags GetAdaptiveDepthFlags(void) const

GetAdaptiveDepthFlags() returns current set of adaptive depth heuristics flags.

bool HasExplicitAnnotsNames() const

CMappedFeat & Set(CAnnot_Collector &collector, const CAnnotObject_Ref &feat_ref)

const TAnnotsNames & GetIncludedAnnotsNames(void) const

bool GetFeatProduct(void) const

Return true if the features should be searched using their product rather than location.

SSeqMapSelector & SetLimitTSE(const CSeq_entry_Handle &tse)

Limit TSE to resolve references.

bool HasIncludedOnlyNamedAnnotAccessions() const

CSeq_id_Handle GetRefSeqid(void) const

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

bool ExtractZoomLevel(const string &full_name, string *acc_ptr, int *zoom_level_ptr)

Extract optional zoom level suffix from named annotation string.

EOverlapType m_OverlapType

bool FeaturePolicyWasApplied(void) const

const TNamedAnnotAccessions & GetNamedAnnotAccessions(void) const

Uint1 TAdaptiveDepthFlags

TSeqPos GetRefEndPosition(void) const

TSeqPos GetPosition(void) const

return position of current segment in sequence

SAnnotSelector & ExcludeNamedAnnotAccession(const string &acc)

bool GetExcludeIfGeneIsSuppressed(void) const

bool MatchType(const CAnnotObject_Info &annot_info) const

Check if type of the annotation matches the selector.

SSeqMapSelector & SetByFeaturePolicy(void)

CConstRef< CSeq_feat > GetSeq_feat(void) const

Get current seq-feat.

const CTSE_Handle & GetUsingTSE(void) const

@ eSortOrder_Reverse

decresing end, decreasing length

@ eSortOrder_Normal

default - increasing start, decreasing length

@ eOverlap_Intervals

default - overlapping of individual intervals

@ eIgnoreUnresolved

Ignore unresolved ids (default)

@ eSearchUnresolved

Search annotations for unresolvable IDs.

@ eFailUnresolved

Throw exception for unresolved ids.

@ eResolve_TSE

default - search only on segments in the same TSE

@ eResolve_All

Search annotations for all referenced sequences.

@ eResolve_None

Do not search annotations on segments.

@ eMaxSearchSegmentsThrow

bool HasSegmentOfType(ESegmentType type) const

@ eSeqRef

reference to Bioseq

bool IsNull(void) const THROWS_NONE

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

void AtomicResetFrom(const TThisType &ref)

Reset reference object to new pointer.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

CRef< C > Ref(C *object)

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

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

bool ReferencedOnlyOnce(void) const THROWS_NONE

Check if object is referenced only once.

TObjectType * GetPointerOrNull(void) THROWS_NONE

Get pointer value.

TObjectType & GetNCObject(void) const

Get object.

void AtomicReleaseTo(TThisType &ref)

Release referenced object to another CRef<> object.

uint64_t Uint8

8-byte (64-bit) unsigned integer

position_type GetLength(void) const

const_iterator begin(void) const

position_type GetTo(void) const

TThisType & CombineWith(const TThisType &r)

position_type GetToOpen(void) const

position_type GetFrom(void) const

static TThisType GetEmpty(void)

TThisType & Set(position_type from, position_type to)

TThisType & SetOpen(position_type from, position_type toOpen)

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.

bool IsRunning(void) const

Check state of stopwatch.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Stop(void)

Suspend the timer.

void Start(void)

Start the timer.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TDesc & GetDesc(void) const

Get the Desc member data.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

bool IsSetLocus(void) const

Official gene symbol Check if a value has been assigned to Locus data member.

bool IsSetDesc(void) const

descriptive name Check if a value has been assigned to Desc data member.

const TLocus & GetLocus(void) const

Get the Locus member data.

bool IsSetTitle(void) const

for user defined label Check if a value has been assigned to Title data member.

TXref & SetXref(void)

Assign a value to Xref data member.

const TKey & GetKey(void) const

Get the Key member data.

bool IsSetComment(void) const

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

TDbxref & SetDbxref(void)

Assign a value to Dbxref data member.

void ResetPartial(void)

Reset Partial data member.

const TData & GetData(void) const

Get the Data member data.

void ResetTitle(void)

Reset Title data member.

bool IsSetQual(void) const

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

const TExts & GetExts(void) const

Get the Exts member data.

bool IsSetExt(void) const

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

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TIds & GetIds(void) const

Get the Ids member data.

TIds & SetIds(void)

Assign a value to Ids data member.

const TTitle & GetTitle(void) const

Get the Title member data.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void ResetExcept(void)

Reset Except data member.

void SetCit(TCit &value)

Assign a value to Cit data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

void ResetExp_ev(void)

Reset Exp_ev 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.

void ResetExcept_text(void)

Reset Except_text data member.

bool IsSetXref(void) const

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

TExts & SetExts(void)

Assign a value to Exts data member.

const TLocation & GetLocation(void) const

Get the Location member data.

E_Choice

Choice variants.

void SetExcept(TExcept value)

Assign a value to Except data member.

void SetExt(TExt &value)

Assign a value to Ext data member.

void SetTitle(const TTitle &value)

Assign a value to Title data member.

void ResetIds(void)

Reset Ids data member.

void ResetExts(void)

Reset Exts data member.

void ResetPseudo(void)

Reset Pseudo data member.

void ResetId(void)

Reset Id data member.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

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.

void SetId(TId &value)

Assign a value to Id data member.

bool IsSetExcept_text(void) const

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

void SetData(TData &value)

Assign a value to Data data member.

bool IsSetExp_ev(void) const

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

void ResetComment(void)

Reset Comment data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsSetIds(void) const

set of Ids; will replace 'id' field Check if a value has been assigned to Ids data member.

void SetExp_ev(TExp_ev value)

Assign a value to Exp_ev data member.

bool IsSetId(void) const

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

TPseudo GetPseudo(void) const

Get the Pseudo member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetPseudo(void) const

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

const TComment & GetComment(void) const

Get the Comment member data.

void ResetExt(void)

Reset Ext data member.

bool IsSetExts(void) const

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

bool IsSetCit(void) const

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

void SetPseudo(TPseudo value)

Assign a value to Pseudo data member.

const TGene & GetGene(void) const

Get the variant data.

TPartial GetPartial(void) const

Get the Partial member data.

void SetExcept_text(const TExcept_text &value)

Assign a value to Except_text data member.

TExcept GetExcept(void) const

Get the Except member data.

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

void ResetProduct(void)

Reset Product data member.

vector< CRef< CGb_qual > > TQual

void ResetXref(void)

Reset Xref data member.

void ResetDbxref(void)

Reset Dbxref data member.

bool IsSetDbxref(void) const

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

TQual & SetQual(void)

Assign a value to Qual data member.

bool IsSetProduct(void) const

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

TExp_ev GetExp_ev(void) const

Get the Exp_ev member data.

void ResetQual(void)

Reset Qual data member.

const TImp & GetImp(void) const

Get the variant data.

void ResetCit(void)

Reset Cit data member.

@ eFrame_not_set

not set, code uses one

void SetTo(TTo value)

Assign a value to To data member.

void SetPoint(TPoint value)

Assign a value to Point data member.

void SetId(TId &value)

Assign a value to Id data member.

void ResetFuzz_to(void)

Reset Fuzz_to data member.

bool IsMix(void) const

Check if variant Mix is selected.

ENa_strand

strand of nucleic acid

const TId & GetId(void) const

Get the Id member data.

void SetId(TId &value)

Assign a value to Id data member.

void SetStrand(TStrand value)

Assign a value to Strand data member.

TFrom GetFrom(void) const

Get the From member data.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

void ResetFuzz(void)

Reset Fuzz data member.

void SetFrom(TFrom value)

Assign a value to From data member.

void ResetStrand(void)

Reset Strand data member.

void ResetFuzz_from(void)

Reset Fuzz_from data member.

virtual void Reset(void)

Reset the whole object.

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 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 IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

void SetStrand(TStrand value)

Assign a value to Strand data member.

void ResetStrand(void)

Reset Strand data member.

const TMix & GetMix(void) const

Get the variant data.

E_Choice

Choice variants.

@ e_not_set

No variant selected.

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

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 whole

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

void timsort(RandomAccessIterator const first, RandomAccessIterator const last)

Same as std::stable_sort(first, last).

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

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

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

string GetProduct(const CProt_ref &prot_ref)

bool operator()(const CAnnotObject_Ref &x, const CAnnotObject_Ref &y) const

CNearnessTester m_TesterForIgnoreFarLocationsForSorting

IFeatComparator * m_FeatComparator

static int GetTypeOrder(CSeqFeatData::E_Choice type, CSeqFeatData::ESubtype subtype)

CAnnotObjectType_Less(const SAnnotSelector *sel, CScope *scope=0)

bool m_DoWeIgnoreFarLocationsForSorting

CAnnotObject_LessReverse(const SAnnotSelector *sel, CScope *scope=0)

CAnnotObjectType_Less type_less

bool operator()(const CAnnotObject_Ref &x, const CAnnotObject_Ref &y) const

static int CompareRanges(TSeqPos x_from, TSeqPos x_to, TSeqPos y_from, TSeqPos y_to)

CAnnotObjectType_Less type_less

CAnnotObject_Less(const SAnnotSelector *sel, CScope *scope=0)

bool operator()(const CAnnotObject_Ref &x, const CAnnotObject_Ref &y) const

static void GetRangeOpen(TSeqPos &out_from, TSeqPos &out_to, const CAnnotObject_Ref &obj_ref)

void x_GetExtremes(TSeqPos &out_from, TSeqPos &out_to, const CAnnotObject_Ref &obj_ref) const

CBioseq_Handle ignore_far_handle

CRef< CObjectFor< CHandleRange > > m_HandleRange

CAnnotObject_Info * m_AnnotObject_Info

Uint2 m_AnnotLocationIndex

TAnnotType GetAnnotType(void) const

const TRangeMap & x_GetRangeMap(size_t index) const

bool x_RangeMapIsEmpty(size_t index) const

size_t x_GetRangeMapCount(void) const

bool operator()(const CSeq_annot_Handle &a, const CSeq_annot_Handle &b) const

bool operator()(const CSeq_annot_Info *a, const CSeq_annot_Info *b) const

bool operator()(const CSeq_annot_Handle &a, const CSeq_annot_Info *b) const

bool operator()(const CSeq_annot_Info *a, const CSeq_annot_Handle &b) const

bool NoMore(const TRange &range) const

bool NotThis(const TRange &range) const

TSeqPos GetFrom(void) const

void UpdateSeq_feat(CRef< CSeq_feat > &seq_feat, const CSeq_annot_SNP_Info &annot_info) const

bool MinusStrand(void) const

TSeqPos GetTo(void) const

bool PlusStrand(void) const

Selector used in CSeqMap methods returning iterators.

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