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

: m_Info(tse.x_GetScopeInfo().GetScopeLock(tse, tse.x_GetTSE_Info()))

: m_Info(tse.x_GetScopeInfo().GetScopeLock(tse,

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processor.

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processor.

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vector<CSeq_annot_EditHandle> annots;

annots.push_back(it->GetEditHandle());

( vector<CSeq_annot_EditHandle>, it, annots ) {

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TCommand(*

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()));

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( entry.

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CBioseq_set_EditHandle –.

CMDReturn< CMD >::TReturn run(CMD *cmd)

Base class for all object manager exceptions.

CBioseq_Handle GetBioseqHandle(const CSeq_id_Handle &id, int get_flag)

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

CConstRef< TObject > GetSeq_entryCore(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &d)

bool AddSeqdesc(CSeqdesc &d)

void AddSeq_descr(const TDescr &v)

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

const TDescr & GetDescr(void) const

E_Choice Which(void) const

bool IsSetDescr(void) const

virtual const CBioObjectId & GetBioObjectId(void) const

CConstRef< TObject > GetCompleteSeq_entry(void) const

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from this TSE.

CSubmit_block & SetTopLevelSubmit_block() const

const CSubmit_block & GetTopLevelSubmit_block() const

More efficient direct access to Seq-submit.sub field.

bool IsTopLevelSeq_submit() const

const CSeq_submit & GetTopLevelSeq_submit() const

Return reference to top-level Seq-submit object Throw an exception if it's not available.

bool CanBeEdited(void) const

Return true if this TSE handle is local to scope and can be edited.

const CTSE_Info & GetTSE_Info(void) const

bool HasParent_Info(void) const

TBlobVersion GetBlobVersion(void) const

const TBlobId & GetBlobId(void) const

IEditSaver * GetEditSaver(const Handle &handle)

#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.

CBioseq_EditHandle GetEditHandle(const CBioseq_Handle &seq)

Get editable Biosec handle by regular one.

CSubmit_block & SetTopLevelSubmit_block(void) const

Seq-submit support.

TSeq ConvertSetToSeq(void) const

Do the same as CollapseSet() when sub-entry is of type bioseq.

const TDescr & GetDescr(void) const

CRef< CSeqdesc > RemoveSeqdesc(const CSeqdesc &v) const

void x_RealResetDescr(void) const

CSeq_annot_EditHandle TakeAnnot(const CSeq_annot_EditHandle &annot) const

Remove the annotation from its location and attach to current one.

friend class CBioseq_set_Handle

TSet SelectSet(TClass set_class=CBioseq_set::eClass_not_set) const

Convert the empty Seq-entry to Bioseq-set.

TSet TakeSet(const TSet &seqset) const

Make the empty Seq-entry be in set state with moving Bioseq-set object from the argument seqset.

void Swap(CSeq_entry_Handle &h)

Reset handle and make it not to point to any seq-entry.

CBioseq_set_EditHandle GetParentBioseq_set(void) const

Get parent bioseq-set edit handle.

const CSeq_submit & GetTopLevelSeq_submit(void) const

void UpdateAnnotations(void) const

Update annotation index after manual modification of the object.

void SelectNone(void) const

Make this Seq-entry to be empty.

const TObjectInfo & GetObjectInfo(void) const

void Remove(void) const

Remove current annot.

void SetClass(TClass v) const

CBioseq_EditHandle AttachBioseq(CBioseq &seq, int index=-1) const

Attach a bioseq.

TSet CopySet(const CBioseq_set_Handle &seqset) const

Make the empty Seq-entry be in set state with given Bioseq-set object.

void AddDescr(TDescr &v) const

CSeq_entry_EditHandle GetSingleSubEntry(void) const

Get edit handle of the sub seq-entry If current seq-entry is not seq-set or has more than one subentr...

E_Choice Which(void) const

const CBioObjectId & GetBioObjectId(void) const

Get unique object id.

void x_RealSetDescr(TDescr &v) const

CSeq_entry_EditHandle TakeEntry(const CSeq_entry_EditHandle &entry, int index=-1) const

Remove seq-entry from its location and attach to current one.

void Remove(void) const

Remove this Seq-entry from parent, or scope if it's top level Seq-entry.

bool IsRemoved(void) const

CSeq_annot_EditHandle AttachAnnot(CSeq_annot &annot) const

Attach an annotation.

TSet ConvertSeqToSet(TClass set_class=CBioseq_set::eClass_not_set) const

Convert the entry from Bioseq to Bioseq-set.

void TakeAllAnnots(const CSeq_entry_EditHandle &src_entry) const

Remove all the annotation from seq-entry and attach to current one.

const CTSE_Handle & GetTSE_Handle(void) const

const CSubmit_block & GetTopLevelSubmit_block(void) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

void Remove(ERemoveMode mode=eRemoveSeq_entry) const

Remove current seqset-entry from its location.

CBioseq_set_Handle GetParentBioseq_set(void) const

Get parent bioseq-set handle.

const CSeq_entry_Info & x_GetInfo(void) const

TSeq SelectSeq(CBioseq &seq) const

Make the empty Seq-entry be in seq state with specified Bioseq object.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from the TSE of this Seq-entry.

bool IsRemoved(void) const

Check if handle points to a removed bioseq.

friend class CBioseq_EditHandle

bool IsTopLevelEntry(void) const

Check if this handle is top-level entry.

CBioseq_EditHandle TakeBioseq(const CBioseq_EditHandle &seq, int index=-1) const

Remove bioseq from its location and attach to current one.

CSeq_entry_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CBioseq_EditHandle CopyBioseq(const CBioseq_Handle &seq, int index=-1) const

Attach a copy of the bioseq.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

void x_RealAddSeq_descr(TDescr &v) const

bool IsTopLevelSeq_submit(void) const

Seq-submit access functions.

CBioseq_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CBioseq_EditHandle CopyBioseq(const CBioseq_Handle &seq, int index=-1) const

Attach a copy of the existing bioseq.

bool x_RealAddSeqdesc(CSeqdesc &v) const

CSeq_entry_EditHandle AttachEntry(CSeq_entry &entry, int index=-1) const

Attach an existing seq-entry.

TSeq CopySeq(const CBioseq_Handle &seq) const

Make the empty Seq-entry be in seq state with specified Bioseq object.

const CBioseq_set_Info & x_GetInfo(void) const

bool IsSetDescr(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

TBlobId GetBlobId(void) const

CSeq_entry_EditHandle CopyEntry(const CSeq_entry_Handle &entry, int index=-1) const

Attach a copy of the existing seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

const CSeq_annot_Info & x_GetInfo(void) const

CSeq_entry_EditHandle TakeEntry(const CSeq_entry_EditHandle &entry, int index=-1) const

Remove seq-entry from its location and attach to current one.

CBioseq_EditHandle TakeBioseq(const CBioseq_EditHandle &seq, int index=-1) const

Remove bioseq from its location and attach to current one.

TBlobVersion GetBlobVersion(void) const

TDescr & SetDescr(void) const

void CollapseSet(void) const

Collapse one level of Bioseq-set.

const CBioseq_Info & x_GetInfo(void) const

CRef< CSeqdesc > x_RealRemoveSeqdesc(const CSeqdesc &v) const

CSeq_entry_EditHandle AddNewEntry(int index) const

Create new empty seq-entry.

CSeq_entry_EditHandle AttachEntry(CSeq_entry &entry, int index=-1) const

Attach an existing seq-entry.

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

CSeq_entry_EditHandle GetParentEntry(void) const

Get parent seq-entry edit handle.

void TakeAllDescr(const CSeq_entry_EditHandle &src_entry) const

Remove all the descritions from seq-entry and attach to current one.

CBioseq_EditHandle AttachBioseq(CBioseq &seq, int index=-1) const

Attach an existing bioseq.

CSeq_entry_EditHandle CopyEntry(const CSeq_entry_Handle &entry, int index=-1) const

Attach a copy of the existing seq-entry.

bool HasParentEntry(void) const

Check if current seq-entry has a parent.

void ResetDescr(void) const

CSeq_entry_Info & x_GetInfo(void) const

CSeq_entry_EditHandle(void)

void Reset(void)

Reset handle and make it not to point to any seq-entry.

CSeq_entry_Handle GetSingleSubEntry(void) const

Get handle of the sub seq-entry If current seq-entry is not seq-set or has more than one subentry exc...

CSeq_annot_EditHandle CopyAnnot(const CSeq_annot_Handle &annot) const

Attach a copy of the annotation.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

bool AddSeqdesc(CSeqdesc &v) const

TSeq TakeSeq(const TSeq &seq) const

Make the empty Seq-entry be in seq state with moving bioseq object from the argument seq.

CScope_Impl & x_GetScopeImpl(void) const

friend class CBioseq_set_EditHandle

CConstRef< CSeq_entry > GetSeq_entryCore(void) const

Get const reference to the seq-entry.

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

CRef< C > Ref(C *object)

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

void Swap(TThisType &ref)

Swaps the pointer with another reference.

#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.

E_Choice

Choice variants.

@ e_not_set

No variant selected.

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