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

35 #include <wx/stattext.h> 36 #include <wx/msgdlg.h> 89 Create

(parent,

id

, caption, pos,

size

, style);

100

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

106

GetSizer()->SetSizeHints(

this

);

149

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

150

itemCBulkCmdDlg1->SetSizer(itemBoxSizer2);

152

wxBoxSizer* itemBoxSizer3 =

new

wxBoxSizer(wxHORIZONTAL);

153

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

155

wxStaticText* itemStaticText1 =

new

wxStaticText( itemCBulkCmdDlg1, wxID_STATIC,

(

"Triplet Codon"

), wxDefaultPosition, wxDefaultSize, 0 );

156

itemBoxSizer3->Add(itemStaticText1, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

158 m_Triplet

new

wxTextCtrl( itemCBulkCmdDlg1,

ID_TEXTCTRL35

, wxEmptyString, wxDefaultPosition, wxSize(40, -1), 0 );

159

itemBoxSizer3->Add(

m_Triplet

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 0);

162

wxBoxSizer* itemBoxSizer4 =

new

wxBoxSizer(wxHORIZONTAL);

163

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

165

wxStaticText* itemStaticText2 =

new

wxStaticText( itemCBulkCmdDlg1, wxID_STATIC,

(

"Amino Acid"

), wxDefaultPosition, wxDefaultSize, 0 );

166

itemBoxSizer4->Add(itemStaticText2, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

168

wxArrayString m_AminoAcidCtrlStrings;

169

m_AminoAcidCtrlStrings.Add(wxEmptyString);

170

m_AminoAcidCtrlStrings.Add(

(

"Alanine"

));

171

m_AminoAcidCtrlStrings.Add(

(

"Asp or Asn"

));

172

m_AminoAcidCtrlStrings.Add(

(

"Cysteine"

));

173

m_AminoAcidCtrlStrings.Add(

(

"Aspartic Acid"

));

174

m_AminoAcidCtrlStrings.Add(

(

"Glutamic Acid"

));

175

m_AminoAcidCtrlStrings.Add(

(

"Phenylalanine"

));

176

m_AminoAcidCtrlStrings.Add(

(

"Glycine"

));

177

m_AminoAcidCtrlStrings.Add(

(

"Histidine"

));

178

m_AminoAcidCtrlStrings.Add(

(

"Isoleucine"

));

179

m_AminoAcidCtrlStrings.Add(

(

"Leu or Ile"

));

180

m_AminoAcidCtrlStrings.Add(

(

"Lysine"

));

181

m_AminoAcidCtrlStrings.Add(

(

"Leucine"

));

182

m_AminoAcidCtrlStrings.Add(

(

"Methionine"

));

183

m_AminoAcidCtrlStrings.Add(

(

"Asparagine"

));

184

m_AminoAcidCtrlStrings.Add(

(

"Pyrrolysine"

));

185

m_AminoAcidCtrlStrings.Add(

(

"Proline"

));

186

m_AminoAcidCtrlStrings.Add(

(

"Glutamine"

));

187

m_AminoAcidCtrlStrings.Add(

(

"Arginine"

));

188

m_AminoAcidCtrlStrings.Add(

(

"Serine"

));

189

m_AminoAcidCtrlStrings.Add(

(

"Threonine"

));

190

m_AminoAcidCtrlStrings.Add(

(

"Selenocysteine"

));

191

m_AminoAcidCtrlStrings.Add(

(

"Valine"

));

192

m_AminoAcidCtrlStrings.Add(

(

"Tryptophan"

));

193

m_AminoAcidCtrlStrings.Add(

(

"Undetermined or atypical"

));

194

m_AminoAcidCtrlStrings.Add(

(

"Tyrosine"

));

195

m_AminoAcidCtrlStrings.Add(

(

"Glu or Gln"

));

196

m_AminoAcidCtrlStrings.Add(

(

"Termination"

));

197 m_AminoAcidCtrl

new

wxChoice( itemCBulkCmdDlg1,

ID_CHOICE14

, wxDefaultPosition, wxSize(100, -1), m_AminoAcidCtrlStrings, 0 );

198

itemBoxSizer4->Add(

m_AminoAcidCtrl

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 0);

234

itemBoxSizer2->Add(

m_OkCancel

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

289 string

pattern =

m_Triplet

->GetValue().ToStdString();

296 if

(pattern.size() < 3 || aa_str.empty())

300 bool

modified =

false

;

304 const CSeq_loc

& loc = fi->GetLocation();

308 const CSeq_feat

& cds = fi->GetOriginalFeature();

325 int

offset_frame = 0;

341 for

(

size_t i

= offset_frame;

< seq.

size

();

+= 3)

350

code_break->

SetAa

().SetNcbieaa(aa_str[0]);

355 for

(

CSeq_loc_CI

loc_iter(loc); loc_iter; ++loc_iter)

357 int len

= loc_iter.GetRange().GetLength();

358 if

(offset <= i && offset + len >

)

360

cb_loc->

SetInt

().SetId().Assign(loc_iter.GetSeq_id());

371 if

(offset <= i + 2 && offset + len >

+ 2)

386

cb_loc->

SetInt

().SetFrom(loc_iter.GetRange().GetFrom());

389

cb_loc->

SetInt

().SetTo(loc_iter.GetRange().GetTo());

395 if

(cb_loc->

IsInt

())

403 tmp

->SetId().Assign(loc_iter.GetSeq_id());

407 tmp

->SetTo(loc_iter.GetRange().GetTo());

414 tmp

->SetFrom(loc_iter.GetRange().GetFrom());

419 tmp

->SetFrom(loc_iter.GetRange().GetFrom());

426 tmp

->SetTo(loc_iter.GetRange().GetTo());

433

code_break->

SetLoc

(*cb_loc);

436

new_feat->

SetData

().SetCdregion().SetCode_break().push_back(code_break);

440 cmd

->AddCommand(*retranslate);

474

new_inst->Assign(prot_bsh.

GetInst

());

478 if

(new_inst->IsSetSeq_data())

480

new_inst->ResetSeq_data();

490

new_inst->ResetExt();

491

new_inst->SetRepr(objects::CSeq_inst::eRepr_raw);

492

new_inst->SetSeq_data().SetNcbieaa().Set(

prot

);

501 cmd

->AddCommand(*chgInst);

User-defined methods of the data storage class.

USING_SCOPE(ncbi::objects)

static bool ShowToolTips()

Should we show tooltips?

COkCancelPanel * m_OkCancel

virtual CRef< CCmdComposite > GetCommand()

virtual string GetErrorMessage()

CAddGlobalCodeBreak()

Constructors.

vector< string > m_AminoAcidList

wxChoice * m_AminoAcidCtrl

bool Create(wxWindow *parent, wxWindowID id=10268, const wxString &caption=_("Add Code Break"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(900, 500), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

~CAddGlobalCodeBreak()

Destructor.

CRef< CCmdComposite > RetranslateCDSCommand(CScope &scope, CSeq_feat &cds)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void CreateControls()

Creates the controls and sizers.

void Init()

Initialises member variables.

objects::CSeq_entry_Handle m_TopSeqEntry

bool Create(wxWindow *parent, wxWindowID id, const wxString &title, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxDEFAULT_FRAME_STYLE, const wxString &name=wxFrameNameStr)

bool GetTopLevelSeqEntryAndProcessor()

static const CTrans_table & GetTransTable(int id)

namespace ncbi::objects::

Seq-loc iterator class â iterates all intervals from a seq-loc in the correct order.

IWorkbench is the central interface in the application framework.

static const char * str(char *buf, int n)

unsigned int TSeqPos

Type for sequence locations and lengths.

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

Set object to copy of another one.

void SetPacked_int(TPacked_int &v)

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsProtein(void) const

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

void SetAa(TAa &value)

Assign a value to Aa data member.

bool IsSetData(void) const

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

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TCode & GetCode(void) const

Get the Code member data.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetFrame(void) const

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

@ eFrame_three

reading frame

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

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

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

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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/add__global__code__break_8cpp_source.html below:

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/addglobalcode__break_8cpp_source.html below: