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

(

.GetType() ) {

& seq_id =

&

(*

.GetSeqId().GetSeqId());

<

THandle>

&

= TTypeChooser::GetCommand(*holder);

<

THandle>

&

= TTypeChooser::GetCommand(*holder);

<

THandle>

.SetAdd_descr(

&

(descr));

<

THandle>

.SetSet_descr(

&

(descr));

<

THandle>

<

THandle>

SetAdd_desc(

&

(desc));

<

THandle>

SetRemove_desc(

&

(desc));

(entry.

()) {

<

T>

<

Holder>

(Holder& holder,

& feat) { holder.SetFeat(feat); }

<

Holder>

(Holder& holder,

& align) { holder.SetAlign(align); }

<

Holder>

(Holder& holder,

& graph) { holder.SetGraph(graph); }

<

T>

TAnnotObjTrait::TCont TCont;

TCont& cont = TAnnotObjTrait::GetCont(*annot);

( cont.size() > 1 ) {

(

TCont, it, cont) {

( !(*it)->Equals(new_obj) ) {

& obj =

&

(**it);

TAnnotObjTrait::Set(

.SetSearch_param().SetObj(), obj);

.SetSearch_param()

<

T>

& nc_value =

&

(

);

<

T>

& nc_value =

&

(old_value);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void transform(Container &c, UnaryFunction *op)

IEditsDBEngine & GetDBEngine()

virtual void ResetBioseqSetRelease(const CBioseq_set_Handle &, ECallMode)

virtual void ResetSeqInstExt(const CBioseq_Handle &, ECallMode)

virtual void Attach(const CBioObjectId &old_id, const CSeq_entry_Handle &entry, const CBioseq_Handle &what, ECallMode)

virtual void AddId(const CBioseq_Handle &, const CSeq_id_Handle &, ECallMode)

ID operation.

virtual void ResetDescr(const CBioseq_Handle &, ECallMode)

virtual void SetBioseqSetDate(const CBioseq_set_Handle &, const CBioseq_set::TDate &, ECallMode)

virtual void RemoveId(const CBioseq_Handle &, const CSeq_id_Handle &, ECallMode)

virtual void CommitTransaction()

Called when a transaction is finished.

virtual void SetBioseqSetId(const CBioseq_set_Handle &, const CBioseq_set::TId &, ECallMode)

virtual void RollbackTransaction()

Called when a transaction should be undone.

virtual void SetBioseqSetColl(const CBioseq_set_Handle &, const CBioseq_set::TColl &, ECallMode)

virtual void SetSeqInstRepr(const CBioseq_Handle &, CSeq_inst::TRepr, ECallMode)

virtual void ResetBioseqSetColl(const CBioseq_set_Handle &, ECallMode)

virtual void ResetBioseqSetDate(const CBioseq_set_Handle &, ECallMode)

virtual void SetBioseqSetRelease(const CBioseq_set_Handle &, const CBioseq_set::TRelease &, ECallMode)

virtual void SetDescr(const CBioseq_Handle &, const CSeq_descr &, ECallMode)

virtual void ResetSeqInst(const CBioseq_Handle &, ECallMode)

virtual void AddDesc(const CBioseq_Handle &, const CSeqdesc &, ECallMode)

virtual void ResetBioseqSetId(const CBioseq_set_Handle &, ECallMode)

virtual void SetSeqInstMol(const CBioseq_Handle &, CSeq_inst::TMol, ECallMode)

virtual void ResetSeqInstTopology(const CBioseq_Handle &, ECallMode)

virtual void Remove(const CSeq_entry_Handle &entry, const CSeq_annot_Handle &what, ECallMode)

virtual void BeginTransaction()

Called when a transaction has just been started.

virtual void ResetSeqInstSeq_data(const CBioseq_Handle &, ECallMode)

virtual void SetSeqInstFuzz(const CBioseq_Handle &info, const CSeq_inst::TFuzz &fuzz, ECallMode)

virtual void SetSeqInstSeq_data(const CBioseq_Handle &info, const CSeq_inst::TSeq_data &data, ECallMode)

virtual void SetSeqInstLength(const CBioseq_Handle &, CSeq_inst::TLength, ECallMode)

virtual void RemoveDesc(const CBioseq_Handle &, const CSeqdesc &, ECallMode)

virtual void ResetSeqInstFuzz(const CBioseq_Handle &, ECallMode)

virtual void Add(const CSeq_annot_Handle &handle, const CSeq_feat &obj, ECallMode)

virtual void Detach(const CSeq_entry_Handle &entry, const CBioseq_Handle &what, ECallMode)

virtual void SetSeqInst(const CBioseq_Handle &, const CSeq_inst &, ECallMode)

CSeq_inst operatoions.

virtual void SetSeqInstHist(const CBioseq_Handle &info, const CSeq_inst::THist &hist, ECallMode)

virtual void Replace(const CSeq_feat_Handle &handle, const CSeq_feat &old_value, ECallMode)

virtual void SetSeqInstStrand(const CBioseq_Handle &info, CSeq_inst::TStrand strand, ECallMode)

virtual void ResetBioseqSetClass(const CBioseq_set_Handle &, ECallMode)

virtual void AddDescr(const CBioseq_Handle &, const CSeq_descr &, ECallMode)

Description operations.

virtual void ResetSeqInstLength(const CBioseq_Handle &, ECallMode)

virtual void ResetSeqInstHist(const CBioseq_Handle &, ECallMode)

virtual void SetSeqInstExt(const CBioseq_Handle &info, const CSeq_inst::TExt &ext, ECallMode)

virtual void ResetSeqInstMol(const CBioseq_Handle &, ECallMode)

virtual void ResetSeqInstStrand(const CBioseq_Handle &, ECallMode)

virtual void ResetIds(const CBioseq_Handle &, const TIds &, ECallMode)

virtual void SetSeqInstTopology(const CBioseq_Handle &info, CSeq_inst::TTopology topology, ECallMode)

virtual void SetBioseqSetLevel(const CBioseq_set_Handle &, CBioseq_set::TLevel, ECallMode)

virtual void ResetSeqInstRepr(const CBioseq_Handle &, ECallMode)

virtual void ResetBioseqSetLevel(const CBioseq_set_Handle &, ECallMode)

virtual void SetBioseqSetClass(const CBioseq_set_Handle &, CBioseq_set::TClass, ECallMode)

CEditsSaver(IEditsDBEngine &)

CSeqEdit_Cmd_AddAnnot –.

CSeqEdit_Cmd_AttachSeqEntry –.

CSeqEdit_Cmd_RemoveAnnot –.

CSeqEdit_Cmd_ReplaceAnnot –.

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

namespace ncbi::objects::

ECallMode

This flag can be used for optimization purpose.

virtual void NotifyIdChanged(const CSeq_id_Handle &id, const string &newblobid)=0

virtual void BeginTransaction()=0

virtual void RollbackTransaction()=0

virtual void CommitTransaction()=0

virtual void SaveCommand(const CSeqEdit_Cmd &cmd)=0

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

static void s_SetSearchParam(CSeqEdit_Cmd_AddAnnot &cmd, const T &new_obj, const CSeq_annot_Handle &handle)

static void s_SetDescr(const THandle &handle, const CSeq_descr &descr, IEditsDBEngine &engine)

#define DEFCHOOSER(type, name)

static void s_AddDesc(const THandle &handle, const CSeqdesc &desc, IEditsDBEngine &engine)

static void s_RemoveAnnot(const CSeq_entry_Handle &entry, const CSeq_annot_Handle &annot, const T &old_value, IEditsDBEngine &engine)

static void s_ResetSetAttr(const CBioseq_set_Handle &handle, CSeqEdit_Cmd_ResetSetAttr::TWhat what, IEditsDBEngine &engine)

static void s_CollectSeqIds(const CSeq_entry &entry, IEditSaver::TIds &ids)

static void s_RemoveDesc(const THandle &handle, const CSeqdesc &desc, IEditsDBEngine &engine)

static void s_AddDescr(const THandle &handle, const CSeq_descr &descr, IEditsDBEngine &engine)

static void s_ResetSeqAttr(const CBioseq_Handle &handle, CSeqEdit_Cmd_ResetSeqAttr::TWhat what, IEditsDBEngine &engine)

static CRef< CSeqEdit_Id > s_Convert(const CBioObjectId &id)

static void s_AddAnnot(const CSeq_annot_Handle &handle, const T &value, IEditsDBEngine &engine)

static CRef< CSeq_id > s_ConvertId(const CSeq_id_Handle &handle)

static void s_ResetDescr(const THandle &handle, IEditsDBEngine &engine)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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.

vector< CSeq_id_Handle > TId

const CSeq_annot_Handle & GetAnnot(void) const

Get an annotation handle for the current seq-graph.

CConstRef< CSeq_graph > GetSeq_graph(void) const

Get constant reference to the current seq-graph.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

E_Choice Which(void) const

const CBioObjectId & GetBioObjectId(void) const

Get unique object id.

CConstRef< CSeq_annot > GetCompleteSeq_annot(void) const

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

CConstRef< CBioseq_set > GetCompleteBioseq_set(void) const

Return the complete bioseq-set object.

const CBioObjectId & GetBioObjectId(void) const

Get unique object id.

CConstRef< CSeq_align > GetSeq_align(void) const

Get const reference to current seq-align.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

const CBioObjectId & GetBioObjectId(void) const

Get unique object id.

const string & GetName(void) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to the seq-annot.

const TId & GetId(void) const

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.

void SetData(TData &value)

Assign a value to Data data member.

TUnique_num & SetUnique_num(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

TBioseqset_id & SetBioseqset_id(void)

Select the variant.

TBioseq_id & SetBioseq_id(void)

Select the variant.

list< CRef< CSeq_id > > TRemove_ids

void SetIndex(TIndex value)

Assign a value to Index data member.

void SetData(TData &value)

Assign a value to Data data member.

void SetSeq_entry(TSeq_entry &value)

Assign a value to Seq_entry data member.

@ eWhat_strand

strand field of seq-inst object

@ eWhat_repr

repr field of seq-inst object

@ eWhat_mol

mol field of seq-inst object

@ eWhat_ext

extr field of seq-inst object

@ eWhat_length

length field of seq-inst object

@ eWhat_hist

hist field of seq-inst object

@ eWhat_fuzz

fuzz field of seq-inst object

@ eWhat_topology

topology field of seq-inst object

@ eWhat_seq_data

seq-data field of seq-inst object

@ eWhat_inst

whole seq-inst object

const TSeq & GetSeq(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetSeq_set(void) const

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

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

@ e_not_set

No variant selected.

const TGraph & GetGraph(void) const

Get the variant data.

ERepr

representation class

list< CRef< CSeq_graph > > TGraph

const TId & GetId(void) const

Get the Id member data.

bool IsSetData(void) const

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

list< CRef< CSeq_align > > TAlign

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.

ETopology

topology of molecule

EMol

molecule class in living organism

const TFtable & GetFtable(void) const

Get the variant data.

EStrand

strandedness in living organism

list< CRef< CSeq_feat > > TFtable

const TData & GetData(void) const

Get the Data member data.

E_Choice Which(void) const

Which variant is currently selected.

static PyObject * Date(PyObject *self, PyObject *args)

const GenericPointer< typename T::ValueType > T2 value

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

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

static void Set(Holder &holder, CSeq_align &align)

CSeq_annot::TData::TAlign TCont

static const TCont & GetCont(const CSeq_annot &annot)

CSeq_annot::TData::TFtable TCont

static const TCont & GetCont(const CSeq_annot &annot)

static void Set(Holder &holder, CSeq_feat &feat)

CSeq_annot::TData::TGraph TCont

static void Set(Holder &holder, CSeq_graph &graph)

static const TCont & GetCont(const CSeq_annot &annot)

SCmdCreator< type > TCmdCreator

static TCommand & PrepareCmd(const CSeq_annot_Handle &annot, CRef< CSeqEdit_Cmd > &cmd)

TCmdCreator::TCommand TCommand

static TCommand & PrepareCmd(const CSeq_annot_Handle &annot, const CSeq_entry_Handle &entry, CRef< CSeqEdit_Cmd > &cmd)

static TCommand & CreateCmd(const THandle &handle, CRef< CSeqEdit_Cmd > &holder)

STypeChooser< type > TTypeChooser

static TCommand & CreateCmd(const THandle &handle, const CBioObjectId &id, CRef< CSeqEdit_Cmd > &holder)

TTypeChooser::TCommand TCommand

string ToString(const wxRect &rc)

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