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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__entry__info_8cpp_source.html below:

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

.x_UpdateComplete();

(

() != which ) {

);

);

(

->GetParentEntry() != &entry ) {

ds.

(obj,

);

(

.Which() ) {

);

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

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

(*it)->x_GetBioseqsIds(ids);

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

(*it)->x_GetBioseqsIds(ids);

(*it)->GetAnnotObjectKeys();

( !ids.empty() &&

== ids.back() ) {

bool IsSetDescr(void) const

const TAnnot & GetAnnot(void) const

virtual void x_ParentAttach(CSeq_entry_Info &parent)

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d)

CRef< CSeqdesc > ReplaceSeqdesc(const CSeqdesc &old_desc, CSeqdesc &new_desc)

const TDescr & GetDescr(void) const

void AddSeq_descr(const TDescr &v)

vector< CRef< CSeq_annot_Info > > TAnnot

const TAnnot & GetLoadedAnnot(void) const

TDesc_CI x_GetFirstDesc(TDescTypeMask types) const

bool AddSeqdesc(CSeqdesc &d)

virtual void x_ParentDetach(CSeq_entry_Info &parent)

const CSeq_entry_Info & GetParentSeq_entry_Info(void) const

void RemoveAnnot(CRef< CSeq_annot_Info > annot)

CRef< CSeq_annot_Info > AddAnnot(CSeq_annot &annot, int chunk_id=0)

bool x_IsEndDesc(TDesc_CI iter) const

TDesc_CI x_GetNextDesc(TDesc_CI iter, TDescTypeMask types) const

vector< CSeq_id_Handle > TId

const TId & GetId(void) const

const TSeq_set & GetSeq_set(void) const

void RemoveEntry(CRef< CSeq_entry_Info > entry)

CRef< CSeq_entry_Info > AddEntry(CSeq_entry &entry, int index, bool set_uniqid=false)

TClass GetClass(void) const

vector< CRef< CSeq_entry_Info > > TSeq_set

void x_Unmap(const CObject *obj, const CTSE_Info_Object *info)

void x_Map(const CObject *obj, const CTSE_Info_Object *info)

Base class for all object manager exceptions.

SAnnotObjectsIndex::TObjectKeys TAnnotObjectKeys

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

TDesc_CI x_GetFirstDesc(TDescTypeMask types) const

void x_DoUpdate(TNeedUpdateFlags flags)

void x_Update(TNeedUpdateFlags flags) const

void RemoveAnnot(CRef< CSeq_annot_Info > annot)

CConstRef< TObject > GetSeq_entryCore(void) const

virtual void x_TSEAttachContents(CTSE_Info &tse_info)

vector< CSeq_id_Handle > TSeqIds

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d)

virtual void x_TSEDetachContents(CTSE_Info &tse_info)

virtual void GetAnnotIds(TSeqIds &ids) const

void x_GetAnnotIds(TSeqIds &ids) const

CSeq_descr::Tdata::const_iterator TDesc_CI

void x_CheckWhich(E_Choice which) const

void x_SetObject(TObject &obj)

bool AddSeqdesc(CSeqdesc &d)

void AddSeq_descr(const TDescr &v)

virtual void x_DSDetachContents(CDataSource &ds)

const CSeq_entry_Info & GetParentSeq_entry_Info(void) const

const CBioseq_Base_Info & x_GetBaseInfo(void) const

CRef< CSeqdesc > ReplaceSeqdesc(const CSeqdesc &old_desc, CSeqdesc &new_desc)

void x_DSMapObject(CConstRef< TObject > obj, CDataSource &ds)

const TDescr & GetDescr(void) const

void x_ParentDetach(CBioseq_set_Info &parent)

CRef< CSeq_entry_Info > AddEntry(CSeq_entry &entry, int index=-1)

CConstRef< TObject > GetSeq_entrySkeleton(void) const

TDesc_CI x_GetNextDesc(TDesc_CI iter, TDescTypeMask types) const

TSeq & SelectSeq(TSeq &seq)

TObject & x_GetObject(void)

virtual void x_DSAttachContents(CDataSource &ds)

CRef< CSeq_annot_Info > AddAnnot(CSeq_annot &annot)

void UpdateAnnotIndex(void) const

const TSeq & GetSeq(void) const

E_Choice Which(void) const

friend class CBioseq_set_Info

void x_AttachContents(void)

CRef< CBioseq_Base_Info > m_Contents

virtual ~CSeq_entry_Info(void)

const TAnnot & GetLoadedAnnot(void) const

void x_SetNeedUpdateContents(TNeedUpdateFlags flags)

friend class CBioseq_Info

virtual void GetSeqAndAnnotIds(TSeqIds &seq_ids, TSeqIds &annot_ids) const

vector< CRef< CSeq_annot_Info > > TAnnot

void x_GetBioseqsIds(TSeqIds &ids) const

void x_UpdateSkeleton() const

void x_DetachContents(void)

virtual void GetBioseqsIds(TSeqIds &ids) const

bool IsSetDescr(void) const

virtual const CBioObjectId & GetBioObjectId(void) const

void x_ParentAttach(CBioseq_set_Info &parent)

void x_SetBioseqChunkId(TChunkId chunk_id)

bool x_IsEndDesc(TDesc_CI iter) const

void x_UpdateAnnotIndexContents(CTSE_Info &tse)

void x_Select(CSeq_entry::E_Choice which, CBioseq_Base_Info *contents)

const TSet & GetSet(void) const

void x_DSUnmapObject(CConstRef< TObject > obj, CDataSource &ds)

const CSeq_entry_Info & GetXrefTSE() const

const CBioseq_set_Info & GetParentBioseq_set_Info(void) const

CConstRef< TObject > GetCompleteSeq_entry(void) const

void RemoveEntry(CRef< CSeq_entry_Info > entry)

virtual void x_DoUpdate(TNeedUpdateFlags flags)

void x_UpdateCore(void) const

virtual void SetBioObjectId(const CBioObjectId &id)

virtual void x_DSDetachContents(CDataSource &ds)

void x_SetNeedUpdate(TNeedUpdateFlags flags)

CDataSource & GetDataSource(void) const

void x_BaseParentAttach(CTSE_Info_Object &parent)

void x_Update(TNeedUpdateFlags flags) const

void x_DetachObject(CTSE_Info_Object &object)

bool HasDataSource(void) const

void x_LoadChunk(TChunkId chunk_id) const

void x_UpdateAnnotIndex(CTSE_Info &tse)

void x_BaseParentDetach(CTSE_Info_Object &parent)

virtual void x_TSEAttachContents(CTSE_Info &tse)

@ fNeedUpdate_children

all fields of children objects

@ fNeedUpdate_descr

specific fields of this object

void x_DSAttach(CDataSource &ds)

virtual void x_DSAttachContents(CDataSource &ds)

void x_TSEAttach(CTSE_Info &tse)

virtual void x_TSEDetachContents(CTSE_Info &tse)

const CTSE_Info & GetTSE_Info(void) const

bool x_DirtyAnnotIndex(void) const

void x_UpdateComplete(void) const

const CTSE_Info_Object & GetBaseParent_Info(void) const

bool HasParent_Info(void) const

void x_TSEDetach(CTSE_Info &tse)

void x_AttachObject(CTSE_Info_Object &object)

virtual const CBioObjectId & GetBioObjectId(void) const

void x_DSDetach(CDataSource &ds)

virtual void x_UpdateAnnotIndexContents(CTSE_Info &tse)

@ kNeedUpdate_bits

number of bits for fields

void UpdateAnnotIndex(const CSeq_id_Handle &id) const

void x_LoadDelayedMainChunk(void) const

vector< CSeq_id_Handle > TSeqIds

Thrown on an attempt to write unassigned data member.

static const struct type types[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

CRef< C > Ref(C *object)

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

void Reset(void)

Reset reference object.

#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.

TSet & SetSet(void)

Select the variant.

E_Choice

Choice variants.

E_Choice Which(void) const

Which variant is currently selected.

TSeq & SetSeq(void)

Select the variant.

@ eClass_parts

parts for 2 or 3

@ eClass_segset

segmented sequence + parts

@ e_not_set

No variant selected.

constexpr auto sort(_Init &&init)

static const int kBioseqChunkId

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