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

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

))

);

processor.

(

TCommand(*

, new_obj));

processor.

(

TCommand(*

, new_obj));

processor.

(

TCommand(*

, new_obj));

);

( annot.

() ) {

);

);

);

vector<CSeq_feat_Handle> feats;

feats.reserve(feat_ci.

());

( feat_ci.

(); feat_ci; ++feat_ci ) {

( feat.

() == *

) {

feats.push_back(feat);

User-defined methods of the data storage class.

Annotation iterators exceptions.

const string & GetName(void) const

size_t GetSize(void) const

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

Base class for all object manager exceptions.

void Commit()

Finish the editing operation.

void x_ClearAnnotCache(void)

CTSE_Handle GetEditHandle(const CTSE_Handle &src_tse)

CConstRef< TObject > GetCompleteSeq_annot(void) const

pair< TAnnotIndex, bool > Add(const CSeq_feat &new_obj)

const CAnnotName & GetName(void) const

CConstRef< TObject > GetSeq_annotCore(void) const

void ReorderFtable(const vector< CSeq_feat_Handle > &feats)

int GetChunkId(void) const

CSeq_feat_EditHandle –.

namespace ncbi::objects::

bool OrderedBefore(const CTSE_Handle &tse) const

bool CanBeEdited(void) const

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

TScopeInfo & x_GetScopeInfo(void) const

virtual const CBioObjectId & GetBioObjectId(void) const

#define NCBI_THROW(exception_class, err_code, message)

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

CScopeTransaction GetTransaction()

CSeq_annot_EditHandle(void)

bool Seq_annot_CanGetDb(void) const

bool IsSeq_table(void) const

CSeq_annot::C_Data::E_Choice Which(void) const

CConstRef< CSeq_graph > GetSeq_graph(void) const

Get constant reference to the current seq-graph.

CSeq_annot_Info & x_GetInfo(void) const

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

void TakeAllAnnots(const CSeq_annot_EditHandle &annot) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

bool IsFtable(void) const

CScopeInfo_Ref< TScopeInfo > m_Info

void Remove(void) const

Remove the Seq-align from Seq-annot.

bool OrderedBefore(const CSeq_annot_Handle &annot) const

More stable comparison - takes loading order in account.

void Remove(void) const

Remove current annot.

void Update(void) const

Update index after manual modification of the object.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

bool Seq_annot_IsSetName(void) const

CScope_Impl & x_GetScopeImpl(void) const

const CTSE_Handle & GetTSE_Handle(void) const

CSeq_align_Handle TakeAlign(const CSeq_align_Handle &handle) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CSeq_graph_Handle AddGraph(const CSeq_graph &new_obj) const

CSeq_graph_Handle TakeGraph(const CSeq_graph_Handle &handle) const

CSeq_feat_EditHandle x_RealAdd(const CSeq_feat &new_obj) const

void ReorderFtable(CFeat_CI &feat_ci) const

void Remove(void) const

Remove the feature from Seq-annot.

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

Complete and return const reference to the current seq-annot.

CSeq_feat_EditHandle AddFeat(const CSeq_feat &new_obj) const

CSeq_annot::TDb Seq_annot_GetDb(void) const

void Remove(void) const

Remove the Seq-graph from Seq-annot.

CConstRef< CSeq_align > GetSeq_align(void) const

Get const reference to current seq-align.

bool Seq_annot_CanGetName(void) const

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

size_t GetSeq_tableNumRows(void) const

const CSeq_annot::TDesc & Seq_annot_GetDesc(void) const

bool Seq_annot_CanGetDesc(void) const

const CSeq_annot::TId & Seq_annot_GetId(void) const

CSeq_annot_EditHandle GetEditHandle(void) const

Get 'edit' version of handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

bool Seq_annot_CanGetId(void) const

const CSeq_annot_Info & x_GetInfo(void) const

const CSeq_annot::TName & Seq_annot_GetName(void) const

CSeq_feat_EditHandle TakeFeat(const CSeq_feat_EditHandle &handle) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const string & GetName(void) const

friend class CSeq_entry_EditHandle

bool Seq_annot_IsSetDb(void) const

CSeq_align_Handle AddAlign(const CSeq_align &new_obj) const

CConstRef< CSeq_annot > GetSeq_annotCore(void) const

bool Seq_annot_IsSetId(void) const

const TObjectInfo & GetObjectInfo(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

bool Seq_annot_IsSetDesc(void) const

const CSeq_annot & x_GetSeq_annotCore(void) const

CSeq_entry_EditHandle GetParentEntry(void) const

Navigate object tree.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

#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.

TNum_rows GetNum_rows(void) const

Get the Num_rows member data.

bool IsAlign(void) const

Check if variant Align is selected.

bool CanGetId(void) const

Check if it is safe to call GetId method.

const TName & GetName(void) const

Get the Name member data.

list< CRef< CAnnot_id > > TId

bool IsSetName(void) const

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

E_Choice

Choice variants.

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.

bool CanGetDesc(void) const

Check if it is safe to call GetDesc method.

bool IsSetDesc(void) const

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

bool IsSetId(void) const

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

TDb GetDb(void) const

Get the Db member data.

bool IsGraph(void) const

Check if variant Graph is selected.

const TSeq_table & GetSeq_table(void) const

Get the variant data.

const TId & GetId(void) const

Get the Id member data.

bool IsFtable(void) const

Check if variant Ftable is selected.

const TData & GetData(void) const

Get the Data member data.

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

bool IsSeq_table(void) const

Check if variant Seq_table is selected.

bool IsIds(void) const

Check if variant Ids is selected.

bool CanGetName(void) const

Check if it is safe to call GetName method.

E_Choice Which(void) const

Which variant is currently selected.

bool IsLocs(void) const

Check if variant Locs is selected.

@ e_Locs

used for communication between tools

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