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

47 #include <wx/stattext.h> 48 #include <wx/statbox.h> 49 #include <wx/button.h> 107

CBulkCmdPanel::Create( parent,

id

, pos,

size

, style );

112

GetSizer()->SetSizeHints(

this

);

163

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxHORIZONTAL);

164

itemCBulkCmdPanel1->SetSizer(itemBoxSizer2);

166

itemBoxSizer2->Add(0, 500, 0, wxALIGN_CENTER_VERTICAL|wxALL, 0);

168

wxBoxSizer* itemBoxSizer4 =

new

wxBoxSizer(wxVERTICAL);

169

itemBoxSizer2->Add(itemBoxSizer4, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

171

wxStaticBox* itemStaticBoxSizer5Static =

new

wxStaticBox(itemCBulkCmdPanel1,

wxID_ANY

(

"RNA Type"

));

172

wxStaticBoxSizer* itemStaticBoxSizer5 =

new

wxStaticBoxSizer(itemStaticBoxSizer5Static, wxVERTICAL);

173

itemBoxSizer4->Add(itemStaticBoxSizer5, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

175

wxArrayString m_RNATypeStrings;

176

m_RNATypeStrings.Add(

(

"preRNA"

));

177

m_RNATypeStrings.Add(

(

"mRNA"

));

178

m_RNATypeStrings.Add(

(

"tRNA"

));

179

m_RNATypeStrings.Add(

(

"rRNA"

));

180

m_RNATypeStrings.Add(

(

"ncRNA"

));

181

m_RNATypeStrings.Add(

(

"tmRNA"

));

182

m_RNATypeStrings.Add(

(

"miscRNA"

));

183 m_RNAType

new

wxChoice( itemStaticBoxSizer5->GetStaticBox(),

ID_CHOICE1

, wxDefaultPosition, wxDefaultSize, m_RNATypeStrings, 0 );

184 m_RNAType

->SetStringSelection(

(

"rRNA"

));

185

itemStaticBoxSizer5->Add(

m_RNAType

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

187

wxBoxSizer* itemBoxSizer7 =

new

wxBoxSizer(wxHORIZONTAL);

188

itemStaticBoxSizer5->Add(itemBoxSizer7, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

190

wxStaticText* itemStaticText8 =

new

wxStaticText( itemStaticBoxSizer5->GetStaticBox(), wxID_STATIC,

(

"ncRNA class"

), wxDefaultPosition, wxDefaultSize, 0 );

191

itemBoxSizer7->Add(itemStaticText8, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

193

wxArrayString m_ncRNAClassStrings;

194 m_ncRNAClass

new

wxComboBox( itemStaticBoxSizer5->GetStaticBox(),

ID_COMBOBOX

, wxEmptyString, wxDefaultPosition, wxDefaultSize, m_ncRNAClassStrings, wxCB_DROPDOWN );

196

itemBoxSizer7->Add(

m_ncRNAClass

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

199

itemBoxSizer4->Add(

m_FieldSizer

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

201

wxStaticText* itemStaticText11 =

new

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

"RNA Name"

), wxDefaultPosition, wxDefaultSize, 0 );

202 m_FieldSizer

->Add(itemStaticText11, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

207

wxStaticText* itemStaticText13 =

new

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

"Comment"

), wxDefaultPosition, wxDefaultSize, 0 );

208 m_FieldSizer

->Add(itemStaticText13, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

210 m_Comment

new

wxTextCtrl( itemCBulkCmdPanel1,

ID_TEXTCTRL10

, wxEmptyString, wxDefaultPosition, wxSize(300, 70), wxTE_MULTILINE );

214

itemBoxSizer4->Add(

m_ButtonsSizer

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

216

wxButton* itemButton16 =

new

wxButton( itemCBulkCmdPanel1,

ID_BUTTON11

(

"Add '18S-ITS-5.8S-ITS-28S' to comment"

), wxDefaultPosition, wxDefaultSize, 0 );

217 m_ButtonsSizer

->Add(itemButton16, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

219

wxButton* itemButton17 =

new

wxButton( itemCBulkCmdPanel1,

ID_BUTTON12

(

"Add '16S-IGS-23S' to comment"

), wxDefaultPosition, wxDefaultSize, 0 );

220 m_ButtonsSizer

->Add(itemButton17, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

225

itemBoxSizer4->Add(

m_Location

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

230 ITERATE

(vector<string>, it, class_vals) {

293

wxStaticText* itemStaticText11 =

new

wxStaticText(

this

, wxID_STATIC,

(

"Gene Symbol"

), wxDefaultPosition, wxDefaultSize, 0 );

294 m_FieldSizer

->Add(itemStaticText11, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

296 m_Locus

new

wxTextCtrl(

this

wxID_ANY

, wxEmptyString, wxDefaultPosition, wxSize(300, -1), 0 );

297 m_FieldSizer

->Add(

m_Locus

, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

299

wxStaticText* itemStaticText13 =

new

wxStaticText(

this

, wxID_STATIC,

(

"Gene Description"

), wxDefaultPosition, wxDefaultSize, 0 );

300 m_FieldSizer

->Add(itemStaticText13, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

302 m_GeneDesc

new

wxTextCtrl(

this

wxID_ANY

, wxEmptyString, wxDefaultPosition, wxSize(300, -1), 0 );

314 bool

need_layout =

false

;

316 while

(num_items > 4) {

317 auto

pos = num_items - 1;

331 bool

need_layout =

false

;

334

wxArrayString m_NameStrings;

335

m_NameStrings.Add(

(

"16S ribosomal RNA"

));

336

m_NameStrings.Add(

(

"18S ribosomal RNA"

));

337

m_NameStrings.Add(

(

"23S ribosomal RNA"

));

338

m_NameStrings.Add(

(

"26S ribosomal RNA"

));

339

m_NameStrings.Add(

(

"28S ribosomal RNA"

));

340

m_NameStrings.Add(

(

"5.8S ribosomal RNA"

));

341

m_NameStrings.Add(

(

"large subunit ribosomal RNA"

));

342

m_NameStrings.Add(

(

"small subunit ribosomal RNA"

));

343 m_rRNAname

new

wxComboBox(

this

wxID_ANY

, wxEmptyString, wxDefaultPosition, wxDefaultSize, m_NameStrings, wxCB_DROPDOWN );

358 bool

need_layout =

false

;

366 if

(!buttons_shown) {

380

wxArrayString m_tRNAStrings;

381

m_tRNAStrings.Add(

(

"A Alanine"

));

382

m_tRNAStrings.Add(

(

"B Asp or Asn"

));

383

m_tRNAStrings.Add(

(

"C Cysteine"

));

384

m_tRNAStrings.Add(

(

"D Aspartic Acid"

));

385

m_tRNAStrings.Add(

(

"E Glutamic Acid"

));

386

m_tRNAStrings.Add(

(

"F Phenylalanine"

));

387

m_tRNAStrings.Add(

(

"G Glycine"

));

388

m_tRNAStrings.Add(

(

"H Histidine"

));

389

m_tRNAStrings.Add(

(

"I Isoleucine"

));

390

m_tRNAStrings.Add(

(

"J Leu or Ile"

));

391

m_tRNAStrings.Add(

(

"K Lysine"

));

392

m_tRNAStrings.Add(

(

"L Leucine"

));

393

m_tRNAStrings.Add(

(

"M Methionine"

));

394

m_tRNAStrings.Add(

(

"N Asparagine"

));

395

m_tRNAStrings.Add(

(

"O Pyrrolysine"

));

396

m_tRNAStrings.Add(

(

"P Proline"

));

397

m_tRNAStrings.Add(

(

"Q Glutamine"

));

398

m_tRNAStrings.Add(

(

"R Arginine"

));

399

m_tRNAStrings.Add(

(

"S Serine"

));

400

m_tRNAStrings.Add(

(

"T Threonine"

));

401

m_tRNAStrings.Add(

(

"U Selenocysteine"

));

402

m_tRNAStrings.Add(

(

"V Valine"

));

403

m_tRNAStrings.Add(

(

"W Tryptophan"

));

404

m_tRNAStrings.Add(

(

"X Undetermined or atypical"

));

405

m_tRNAStrings.Add(

(

"Y Tyrosine"

));

406

m_tRNAStrings.Add(

(

"Z Glu or Gln"

));

407 m_tRNAname

new

wxChoice(

this

wxID_ANY

, wxDefaultPosition, wxDefaultSize, m_tRNAStrings, 0 );

425 m_RNAname

new

wxTextCtrl(

this

wxID_ANY

, wxEmptyString, wxDefaultPosition, wxSize(300, -1), 0 );

447

comment +=

"contains small subunit ribosomal RNA, internal transcribed spacer 1, 5.8S ribosomal RNA, internal transcribed spacer 2, and large subunit ribosomal RNA"

;

462

comment +=

"contains 16S ribosomal RNA, 16S-23S ribosomal RNA intergenic spacer, and 23S ribosomal RNA"

;

469 rna

->SetExt().SetTRNA();

474 char a

= aa.c_str()[0];

475 rna

->SetExt().SetTRNA().SetAa().SetNcbieaa(

);

514 string

rna_name =

""

;

536

objects::CBioseq_CI b_iter(

m_TopSeqEntry

, objects::CSeq_inst::eMol_na);

537 for

( ; b_iter ; ++b_iter ) {

551 string

gene_symbol =

""

;

555 string

gene_desc =

""

;

566

rna_ref->

SetExt

().SetGen();

568

rna_ref->

SetExt

().SetGen().SetProduct(rna_name);

571

rna_ref->

SetExt

().SetGen().SetClass(ncrna_class);

581

rna_ref->

SetExt

().SetName(rna_name);

588 rna

->SetData().SetRna().Assign(*rna_ref);

594 rna

->SetComment(comment);

597 rna

->SetLocation().Assign(*loc);

600 rna

->SetPartial(

true

);

607

new_gene->SetData().SetGene().SetLocus(gene_symbol);

608

new_gene->SetData().SetGene().SetDesc(gene_desc);

609

new_gene->SetLocation().Assign(*loc);

612

new_gene->SetPartial(

true

);

623 return "Must specify rRNA product name!"

;

625 return "Unknown error"

;

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

USING_SCOPE(ncbi::objects)

static void s_SettRNAProduct(string aa, CRef< CRNA_ref > rna)

CBulkLocationPanel * m_Location

bool m_add_location_panel

virtual bool ShouldAddToExisting()

virtual CRef< objects::CSeq_loc > GetLocForBioseq(const objects::CBioseq &bioseq)

wxBoxSizer * m_ButtonsSizer

virtual string GetErrorMessage()

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void OnAdd16StoComment(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON12

wxBoxSizer * m_RNANameSizer

wxFlexGridSizer * m_FieldSizer

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

objects::CRNA_ref::TType x_GetRnaType()

void CreateControls()

Creates the controls and sizers.

objects::CSeq_entry_Handle m_TopSeqEntry

bool Create(wxWindow *parent, wxWindowID id=10062, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

Creation.

~CBulkRNAAddPanel()

Destructor.

bool x_RemoveGeneFields()

void Init()

Initialises member variables.

wxComboBox * m_ncRNAClass

void AddOneCommand(const objects::CBioseq_Handle &bsh, CRef< CCmdComposite > cmd) override

CBulkRNAAddPanel()

Constructors.

void OnSelectRNAType(wxCommandEvent &event)

wxEVT_COMMAND_CHOICE_SELECTED event handler for ID_CHOICE1

void OnAdd18SToComment(wxCommandEvent &event)

wxEVT_COMMAND_BUTTON_CLICKED event handler for ID_BUTTON11

virtual CRef< CCmdComposite > GetCommand()

static bool ShowToolTips()

Should we show tooltips?

static vector< string > GetncRNAClassList()

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

static string & ToUpper(string &str)

Convert string to upper case â string& version.

EType

type of RNA feature

void SetExt(TExt &value)

Assign a value to Ext data member.

void SetType(TType value)

Assign a value to Type data member.

@ eType_ncRNA

non-coding RNA; subsumes snRNA, scRNA, snoRNA

constexpr bool empty(list< Ts... >) noexcept

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

bool AlreadyHasFeature(objects::CBioseq_Handle bh, string key, string comment)

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bulk__rna__add__panel_8cpp_source.html below:

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bulkrnaadd__panel_8cpp_source.html below: