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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/create__protein__id_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/create_protein_id.cpp Source File

((*id_it)->IsGeneral() && (*id_it)->GetGeneral().IsSetDb() &&

(*id_it)->GetGeneral().GetDb() !=

&& (*id_it)->GetGeneral().GetDb() !=

&& (*id_it)->GetGeneral().GetDb() !=

)

existing_db = (*id_it)->GetGeneral().GetDb();

(!existing_db.empty())

= wxGetTextFromUser(

(

),

(

), wxString(existing_db), parent).ToStdString();

(locus_tag.empty())

new_feat->

(orig_feat);

->SetGeneral().SetDb(

);

->SetGeneral().SetTag().SetStr(locus_tag);

(!prot_bsh || !prot_bsh.

())

((*id_it)->IsGeneral() && (*id_it)->GetGeneral().IsSetDb() &&

(*id_it)->GetGeneral().GetDb() !=

&& (*id_it)->GetGeneral().GetDb() !=

&& (*id_it)->GetGeneral().GetDb() !=

)

((*id_it)->IsLocal())

new_seq->

().push_back(

);

((*prot_feat)->IsSetData() && (*prot_feat)->GetData().IsProt() && (*prot_feat)->GetLocation().GetId()->IsLocal() && (*prot_feat)->GetLocation().GetId()->Match(*old_id))

(*prot_feat)->SetLocation().SetId(*

);

new_prot->

(*new_seq);

(dlg.ShowModal() != wxID_OK)

create_protein_ids =

;

ss << prefix <<

<< std::setw(4) << std::setfill(

) <<

;

new_feat->

(*gene);

new_feat->

().SetGene().SetLocus_tag(locus_tag);

new_feat->

().SetGene().SetLocus_tag(locus_tag);

loc->

(feat_ci->GetLocation());

(feat_ci->IsSetPartial() && feat_ci->GetPartial()) {

(create_protein_ids)

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxDialog::Create( parent,

, caption, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemDialog1->SetSizer(itemBoxSizer2);

wxBoxSizer* itemBoxSizer3 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer3, 0, wxALIGN_LEFT|wxALL, 5);

wxStaticText* itemStaticText4 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer3->Add(itemStaticText4, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer3->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer6 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer6, 0, wxALIGN_LEFT|wxALL, 5);

itemBoxSizer6->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer8 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer8, 0, wxALIGN_LEFT|wxALL, 5);

wxStaticText* itemStaticText9 =

wxStaticText( itemDialog1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer8->Add(itemStaticText9, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer8->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer11 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer11, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxButton* itemButton12 =

wxButton( itemDialog1, wxID_OK,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer11->Add(itemButton12, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxButton* itemButton13 =

wxButton( itemDialog1, wxID_CANCEL,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer11->Add(itemButton13, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

static void apply(CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, wxWindow *parent)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

static bool ShowToolTips()

Should we show tooltips?

CCreateLocusTagGenesDlg()

Constructors.

void CreateControls()

Creates the controls and sizers.

bool Create(wxWindow *parent, wxWindowID id=10000, const wxString &caption=_("Create locus-tag genes"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

wxCheckBox * m_CreateProtIds

~CCreateLocusTagGenesDlg()

Destructor.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void Init()

Initialises member variables.

static void create_protein_ids(CSeq_feat_Handle fh, const string &dbname, const string &locus_tag, CScope &scope, CRef< CCmdComposite > cmd)

static void apply(CSeq_entry_Handle tse, ICommandProccessor *cmdProcessor, wxWindow *parent)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

namespace ncbi::objects::

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

#define ID_CREATE_LOCUSTAG_GENE_PREFIX

#define ID_CREATE_LOCUSTAG_GENES_PROT_ID

#define ID_CREATE_LOCUSTAG_GENE_DATABASE

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

Set object to copy of another one.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

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

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

virtual CConstRef< CSeq_feat > GetSeq_feat(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

virtual const CSeq_loc & GetProduct(void) const

bool IsSetProduct(void) const

bool IsProtein(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CScope & GetScope(void) const

Get scope this handle belongs to.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TGene & GetGene(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

TSeq & SetSeq(void)

Select the variant.

TId & SetId(void)

Assign a value to Id data member.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

const struct ncbi::grid::netcache::search::fields::SIZE size

Utility macros and typedefs for exploring NCBI objects from seq.asn.

#define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQID_ON_BIOSEQ EDIT_EACH_SEQID_ON_BIOSEQ.

#define EDIT_EACH_SEQFEAT_ON_SEQANNOT(Itr, Var)

#define EDIT_EACH_SEQANNOT_ON_BIOSEQ(Itr, Var)

#define EDIT_EACH_SEQID_ON_BIOSEQ(Itr, Var)

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