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

&

(c);

( it->first == 0 ) {

m_TotalType.insert(

);

m_TotalLocation.

(loc);

TTypeSet m_TotalType;

TTotalLocation m_TotalLocation;

SSplitAnnotInfo

vector<SAnnotTypeSelector> TTypeSet;

SAllAnnotTypes

vector<SAnnotTypeSelector> TTypeSet;

SAllAnnotTypes(

)

(

.GetAnnotType() ) {

m_FeatTypes[

.GetFeatType()].insert(

.GetFeatSubtype());

(

&& 0);

Add(

TTypeSet&

)

( TFeatTypes, tit, m_FeatTypes ) {

TFeatType

= tit->first;

TSubtypes& subtypes = tit->second;

( !all_subtypes ) {

all_subtypes =

;

= TSubtype(

+1) ) {

subtypes.find(

) == subtypes.end() ) {

all_subtypes =

;

type_info->SetType(

);

( !all_subtypes ) {

( TSubtypes, stit, subtypes ) {

type_info->SetSubtypes().push_back(*stit);

dst.push_back(type_info);

TFeatTypes m_FeatTypes;

vector<SAnnotTypeSelector> TTypeSet;

(

&& 0);

(

.IsSetFeat_subtype() ) {

m_AllAnnots[it->first].Add(sel, it->second);

SplitInfo(

)

( TAllAnnots, it, m_AllAnnots ) {

it->second.m_TotalType) {

type_set.push_back(*tit);

m_SplitAnnots[type_set].Add(it->first,

it->second.m_TotalLocation);

TAllAnnots m_AllAnnots;

TSplitAnnots m_SplitAnnots;

TFeatIdInt;

TFeatIdStr;

vector<SAnnotTypeSelector> TTypeSet;

pair<TTypeSet, TTypeSet> TTypeSets;

vector<TFeatIdInt> TFeatIdsInt;

vector<TFeatIdStr> TFeatIdsStr;

TTypeSets&

= m_AllIdsInt[

.GetId()];

(id_type == eFeatId?

.first:

.second)

.push_back(feat_type);

TTypeSets&

= m_AllIdsStr[

.GetStr()];

(id_type == eFeatId?

.first:

.second)

.push_back(feat_type);

Add(

, **id_it, eFeatId);

( (*xref_it)->IsSetId() )

Add(

, (*xref_it)->GetId(), eXrefId);

clean(TTypeSet&

)

clean(TFeatIdsInt& ids)

(ids.begin(), ids.end());

ids.erase(unique(ids.begin(), ids.end()), ids.end());

clean(TFeatIdsStr& ids)

(ids.begin(), ids.end());

ids.erase(unique(ids.begin(), ids.end()), ids.end());

SplitInfo(

)

clean(it->second.first);

clean(it->second.second);

m_SplitIds[it->second].first.push_back(it->first);

clean(it->second.first);

clean(it->second.second);

m_SplitIds[it->second].second.push_back(it->first);

clean(it->second.first);

clean(it->second.second);

TAllIdsInt m_AllIdsInt;

TAllIdsStr m_AllIdsStr;

TSplitIds m_SplitIds;

<

Func>

ForEachGiRange(

TGiSet& gis, Func func)

( gi_count == 0 || *it != gi_start +

(

, gi_count) ) {

( gi_count > 0 ) {

func(gi_start, gi_count);

( gi_count > 0 ) {

func(gi_start, gi_count);

SetRange(

& obj,

& range)

obj.SetStart(range.

());

TRangeSet& range_set)

( TRangeSet, it, range_set ) {

TRangeSet& range_set)

gi =

.GetGi();

( range_set.size() == 1 ) {

interval.

(gi);

SetRange(interval, *range_set.begin());

seq_ints.

(gi);

AddIntervals(seq_ints.

(), range_set);

( range_set.size() == 1 ) {

SetRange(interval, *range_set.begin());

AddIntervals(seq_ints.

(), range_set);

loc->SetWhole_gi(

.GetGi());

FAddGiRangeToSeq_loc

{ SEPARATE = 3 };

operator()(

start,

)

(

<= SEPARATE ) {

FAddGiRangeToBioseqIds

{ SEPARATE = 2 };

operator()(

start,

)

(

<= SEPARATE ) {

m_Ids.Set().push_back(elem);

elem->SetGi_range().SetStart(start);

elem->SetGi_range().SetCount(

);

m_Ids.Set().push_back(elem);

ForEachGiRange(whole_gi_set, FAddGiRangeToSeq_loc(loc));

( TIntervalSet, it, interval_set ) {

gi_set.insert(it->GetGi());

id_set.insert(it->GetSeqId());

ForEachGiRange(gi_set, FAddGiRangeToBioseqIds(ret));

( TLessIdSet, it, id_set ) {

elem->SetSeq_id(

&

(**it));

ret.

().push_back(elem);

ret.

().push_back(*it);

pair<TBioseqs, TBioseq_sets> TPlaces;

AddPlace(TPlaces& places,

& place)

& range)

range == range.

() ||

TIntervalSet interval_set;

range = it->second.GetTotalRange();

(

(it->first, range) ) {

( it->first.IsGi() ) {

whole_gi_set.insert(it->first.GetGi());

whole_id_set.

(it->first);

interval_set[it->first].insert(range);

(loc, whole_gi_set);

(loc, whole_id_set);

(loc, interval_set);

TIntervalSet interval_set;

(

(id_it->first, range) ) {

( id_it->first.IsGi() ) {

whole_gi_set.insert(id_it->first.GetGi());

whole_id_set.

(id_it->first);

interval_set[id_it->first].insert(range);

(loc, whole_gi_set);

(loc, whole_id_set);

(loc, interval_set);

interval.

(

.GetGi());

SetRange(interval, range);

SetRange(interval, range);

(*loc,

, range);

->SetId().SetSeq_id(

&

(*

));

AddBioseqIds(*ret, ids);

AddBioseq_setIds(*ret, ids);

TDescTypeMask;

TDescPlaces all_descrs;

TPlaces all_annot_places;

TAllAnnots all_annots;

TBioseqPlaces all_bioseqs;

TPlaces all_assemblies;

& place_id = it->first;

TDescTypeMask desc_type_mask = 0;

dst.

().push_back(*

);

desc_type_mask |= (1<<(**i).Which());

AddPlace(all_descrs[desc_type_mask], place_id);

& place_id = it->first;

AddPlace(all_annot_places, place_id);

dst.push_back(annot);

all_annots[name].Add(*annot, *

);

& place_id = it->first;

( !piece || start != p_end ) {

(p_start, p_end-1),

dst.push_back(piece);

p_start = p_end = start;

piece->SetStart(p_start);

piece->SetData().push_back(

);

(p_start, p_end-1),

dst.push_back(piece);

& place_id = it->first;

TBioseqIds& ids = all_bioseqs[place_id];

& seq = *bit->m_Bioseq;

dst.push_back(

(

*

(&seq)));

& place_id = it->first;

AddPlace(all_assemblies, place_id);

nit->second.SplitInfo();

( annot_name.

() ) {

SAllAnnotTypes

;

.Add(it->first);

(

.m_Align ) {

(

.m_Graph ) {

( !

.m_FeatTypes.empty() ) {

chunk_content.push_back(content);

feat_ids.SplitInfo();

( SFeatIds::TSplitIds, it, feat_ids.m_SplitIds ) {

( !it->first.first.empty() ) {

SAllAnnotTypes

;

.Add(it->first.first);

.SetFeatTypes(info_ids->SetFeat_types());

( !it->first.second.empty() ) {

SAllAnnotTypes

;

.Add(it->first.second);

.SetFeatTypes(info_ids->SetXref_types());

( SFeatIds::TFeatIdsInt, fit, it->second.first ) {

info_ids->SetLocal_ids().push_back(*fit);

( SFeatIds::TFeatIdsStr, fit, it->second.second ) {

info_ids->SetLocal_str_ids().push_back(*fit);

store.push_back(info_ids);

chunk_content.push_back(content);

( !all_descrs.empty() ) {

( TDescPlaces, tmit, all_descrs ) {

( !tmit->second.first.empty() ) {

( !tmit->second.second.empty() ) {

chunk_content.push_back(content);

( !all_annot_places.first.empty() ||

!all_annot_places.second.empty() ) {

( !all_annot_places.first.empty() ) {

( !all_annot_places.second.empty() ) {

chunk_content.push_back(content);

( !all_data.

() ) {

(content->SetSeq_data(), all_data);

chunk_content.push_back(content);

( !all_bioseqs.empty() ) {

( TBioseqPlaces, it, all_bioseqs ) {

place->SetBioseq_set(it->first.GetBioseq_setId());

places.push_back(place);

chunk_content.push_back(content);

( !all_assemblies.first.empty() ) {

chunk_content.push_back(content);

dst_chunk_data.push_back(it->second);

dst_chunk_content.push_back(*it);

( seq_it->second.m_Bioseq ) {

dst = &seq_it->second.m_Bioseq->SetDescr();

dst = &seq_it->second.m_Bioseq_set->SetDescr();

dst->

().insert(dst->

().end(),

src.

().begin(), src.

().end());

( seq_it->second.m_Bioseq ) {

seq_it->second.m_Bioseq->SetAnnot().push_back(annot);

seq_it->second.m_Bioseq_set->SetAnnot().push_back(annot);

(seq_it->second.m_Bioseq);

& inst = seq_it->second.m_Bioseq->SetInst();

range = j->GetRange();

TLiterals::iterator iter = literals.find(range.

());

(iter != literals.end());

( seq_it->second.m_Bioseq );

dst = &seq_it->second.m_Bioseq->SetInst().SetHist().SetAssembly();

dst->insert(dst->end(), src.begin(), src.end());

annot->

().SetFtable()

(

&& 0);

User-defined methods of the data storage class.

static void AddLoc(CRef< CSeq_loc > &loc, CRef< CSeq_loc > loc2)

User-defined methods of the data storage class.

set< CRef< CSeq_id >, PPtrLess< CRef< CSeq_id > >> TIdSet

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

const string & GetName(void) const

CID2S_Chunk_Data & GetChunkData(TChunkData &chunk_data, const CPlaceId &place_id)

void AttachToSkeleton(const SChunkInfo &info)

CRef< CMasterSeqSegments > m_Master

static size_t CountAnnotObjects(const CSeq_annot &annot)

vector< CAnnotObject_SplitInfo > TAnnotObjects

CRef< CSeq_annot > MakeSeq_annot(const CSeq_annot &src, const TAnnotObjects &objs)

void SetLoc(CID2S_Seq_loc &loc, const CHandleRangeMap &ranges) const

CBlobSplitterImpl(const SSplitterParams &params)

void MakeID2Chunk(TChunkId id, const SChunkInfo &info)

CRef< CID2S_Bioseq_set_Ids > MakeBioseq_setIds(const set< int > &ids) const

TSeqPos GetLength(const CSeq_data &src) const

bool IsWhole(const CSeq_id_Handle &id, const TRange &range) const

CRef< CSeq_entry > m_Skeleton

vector< CRef< CID2S_Chunk_Content > > TChunkContent

CRef< CID2S_Split_Info > m_Split_Info

CRef< CID2S_Bioseq_Ids > MakeBioseqIds(const set< CSeq_id_Handle > &ids) const

void MakeID2SObjects(void)

CRef< CID2S_Seq_loc > MakeLoc(const CSeqsRange &range) const

void AddRange(const CSeq_id_Handle &h, const TRange &range, ENa_strand strand)

CID2S_Bioseq_place_Info –.

CID2S_Bioseq_set_Ids –.

CID2S_Feat_type_Info –.

CID2S_Seq_annot_Info –.

CID2S_Seq_annot_place_Info –.

CID2S_Seq_assembly_Info –.

CID2S_Seq_descr_Info –.

CID2S_Seq_feat_Ids_Info –.

CID2S_Seq_id_Interval –.

CID2S_Sequence_Piece –.

void Add(const COneSeqRange &range)

bool IsBioseq_set(void) const

bool IsBioseq(void) const

TBioseq_setId GetBioseq_setId(void) const

const TBioseqId & GetBioseqId(void) const

ESubtype GetSubtype(void) const

static E_Choice GetTypeFromSubtype(ESubtype subtype)

@ eSubtype_bad

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

static bool IsGoodFeatTable(const CSeq_table &table)

static CAnnotName GetName(const CSeq_annot &annot)

static size_t CountAnnotObjects(const CSeq_annot &annot)

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

namespace ncbi::objects::

void Add(const CSeq_id_Handle &id, const COneSeqRange &loc)

void AddChunk(const CID2S_Chunk_Id &id, const CID2S_Chunk &chunk)

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

container_type::iterator iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

static const struct type types[]

#define GI_FROM(T, value)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

const TSeqPos kInvalidSeqPos

Define special value for invalid sequence position.

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

Set object to copy of another one.

ENetStorageObjectLocation

Enumeration that indicates the current location of the object.

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.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TSeqPos GetBioseqLength(void) const

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

TObjectType & GetNCObject(void) const

Get object.

position_type GetLength(void) const

TThisType & SetToOpen(position_type toOpen)

position_type GetToOpen(void) const

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.

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

Templatized initialization from a string literal.

TFrom GetFrom(void) const

Get the From member data.

list< CRef< CSeq_align > > TAssembly

void SetName(const TName &value)

Assign a value to Name data member.

TBioseqs & SetBioseqs(void)

Assign a value to Bioseqs data member.

TLoc_set & SetLoc_set(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

void SetType_mask(TType_mask value)

Assign a value to Type_mask data member.

void SetBioseq_sets(TBioseq_sets &value)

Assign a value to Bioseq_sets data member.

list< CRef< CID2S_Interval > > TInts

TSeq_id_interval & SetSeq_id_interval(void)

Select the variant.

TAnnots & SetAnnots(void)

Assign a value to Annots data member.

void SetBioseqs(TBioseqs &value)

Assign a value to Bioseqs data member.

TWhole_gi_range & SetWhole_gi_range(void)

Select the variant.

list< CRef< CID2S_Bioseq_place_Info > > TBioseq_place

TGi_interval & SetGi_interval(void)

Select the variant.

list< CRef< CID2S_Chunk_Data > > TData

void SetGi(TGi value)

Assign a value to Gi data member.

void SetSeq_id(TSeq_id &value)

Assign a value to Seq_id data member.

void SetSeq_loc(TSeq_loc &value)

Assign a value to Seq_loc data member.

TAssembly & SetAssembly(void)

Assign a value to Assembly data member.

TInts & SetInts(void)

Assign a value to Ints data member.

void SetBioseqs(TBioseqs &value)

Assign a value to Bioseqs data member.

void SetCount(TCount value)

Assign a value to Count data member.

list< CRef< CBioseq > > TBioseqs

void SetBioseq_sets(TBioseq_sets &value)

Assign a value to Bioseq_sets data member.

TChunks & SetChunks(void)

Assign a value to Chunks data member.

void SetStart(TStart value)

Assign a value to Start data member.

TData & SetData(void)

Assign a value to Data data member.

TWhole_gi & SetWhole_gi(void)

Select the variant.

TFeat & SetFeat(void)

Assign a value to Feat data member.

TWhole_seq_id & SetWhole_seq_id(void)

Select the variant.

list< CRef< CSeq_annot > > TAnnots

list< CRef< CID2S_Seq_feat_Ids_Info > > TFeat_ids

void SetGi(TGi value)

Assign a value to Gi data member.

TSeq_data & SetSeq_data(void)

Assign a value to Seq_data data member.

void SetSeq_id(TSeq_id &value)

Assign a value to Seq_id data member.

void SetGraph(void)

Set NULL data member (assign 'NULL' value to Graph data member).

list< CRef< CID2S_Sequence_Piece > > TSeq_data

void SetDescr(TDescr &value)

Assign a value to Descr data member.

TInts & SetInts(void)

Assign a value to Ints data member.

void SetAlign(void)

Set NULL data member (assign 'NULL' value to Align data member).

void SetBioseqs(TBioseqs &value)

Assign a value to Bioseqs data member.

list< CRef< CID2S_Chunk_Content > > TContent

E_Choice Which(void) const

Which variant is currently selected.

Tdata & Set(void)

Assign a value to data member.

@ e_Loc_set

combination of locations

@ e_not_set

No variant selected.

const TIds & GetIds(void) const

Get the Ids member data.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsSetXref(void) const

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

E_Choice

Choice variants.

bool IsLocal(void) const

Check if variant Local is selected.

const TData & GetData(void) const

Get the Data member data.

list< CRef< CFeat_id > > TIds

bool IsSetIds(void) const

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

bool IsSetId(void) const

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

const TXref & GetXref(void) const

Get the Xref member data.

vector< CRef< CSeqFeatXref > > TXref

@ e_not_set

No variant selected.

E_Choice Which(void) const

Which variant is currently selected.

TLiteral & SetLiteral(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeqdesc > > Tdata

list< CRef< CSeq_align > > TAssembly

bool IsSetSeq_data(void) const

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

const TGraph & GetGraph(void) const

Get the variant data.

void SetName(const TName &value)

Assign a value to Name data member.

list< CRef< CSeq_graph > > TGraph

void SetDesc(TDesc &value)

Assign a value to Desc data member.

void SetExt(TExt &value)

Assign a value to Ext data member.

const TName & GetName(void) const

Get the Name member data.

list< CRef< CAnnot_id > > TId

const TLiteral & GetLiteral(void) const

Get the variant data.

bool IsSetName(void) const

source if "other" above Check if a value has been assigned to Name data member.

const TId & GetId(void) const

Get the Id member data.

bool IsSetExt(void) const

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

list< CRef< CSeq_align > > TAlign

const Tdata & Get(void) const

Get the member data.

bool IsSetDb(void) const

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

const TDesc & GetDesc(void) const

Get the Desc member data.

list< CRef< CSeq_id > > TId

bool IsSetDesc(void) const

used only for stand alone Seq-annots Check if a value has been assigned to Desc data member.

const TAlign & GetAlign(void) const

Get the variant data.

bool IsSetId(void) const

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

void SetDb(TDb value)

Assign a value to Db data member.

const TExt & GetExt(void) const

Get the Ext member data.

E_Choice Which(void) const

Which variant is currently selected.

TDb GetDb(void) const

Get the Db member data.

const TSeq_table & GetSeq_table(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

E_Choice Which(void) const

Which variant is currently selected.

const TFtable & GetFtable(void) const

Get the variant data.

list< CRef< CSeq_feat > > TFtable

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

Tdata & Set(void)

Assign a value to data member.

bool IsSetSeq_data(void) const

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

list< CRef< CDelta_seq > > Tdata

TId & SetId(void)

Assign a value to Id data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

E_Choice Which(void) const

Which variant is currently selected.

@ e_MaxChoice

== e_Modelev+1

@ e_Literal

a piece of sequence

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

constexpr auto sort(_Init &&init)

ENetStorageObjectLocation TLocation

Int4 delta(size_t dimension_, const Int4 *score_)

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

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

CRef< CSeq_loc > MakeLoc(const char *text)

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

vector< CBioseq_SplitInfo > TPlaceBioseq

vector< CSeq_data_SplitInfo > TPlaceSeq_data

vector< CSeq_hist_SplitInfo > TPlaceSeq_hist

vector< CSeq_descr_SplitInfo > TPlaceSeq_descr

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