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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/sequencingtechnologypanel_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/edit/sequencingtechnologypanel.cpp Source File

42 #include <wx/checkbox.h> 43 #include <wx/textctrl.h> 44 #include <wx/stattext.h> 45 #include <wx/valtext.h> 46 #include <wx/listctrl.h> 47 #include <wx/statbox.h> 50 #include <wx/bitmap.h> 52 #include <wx/toplevel.h> 53 #include <wx/scrolwin.h> 54 #include <wx/hyperlink.h> 103 m_User

new

objects::CUser_object();

119

wxPanel::Create( parent,

id

, pos,

size

, style );

124

GetSizer()->SetSizeHints(

this

);

154 bool

replace_all =

false

;

155

wxSizer *sizer =

NULL

;

156

wxWindow *win = GetParent();

158

sizer = win->GetSizer();

162

wxSizerItemList& itemList = sizer->GetChildren();

163 for

(

size_t i

= 0;

< itemList.size();

++)

165

wxCheckBox* c_btn =

dynamic_cast<

wxCheckBox*

>

(itemList[

]->GetWindow());

166 if

(c_btn && c_btn->GetLabel() ==

(

"Replace All"

))

168

replace_all = c_btn->GetValue();

217

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

218

itemPanel1->SetSizer(itemBoxSizer2);

220

wxArrayString standardCommentCtrlStrings;

222 if

(structuredCommentRules)

225

standardCommentCtrlStrings.Add(wxEmptyString);

231

standardCommentCtrlStrings.Add(wxString(prefix));

239

wxStaticBox* itemStaticBoxSizer3Static =

new

wxStaticBox(itemPanel1,

wxID_ANY

(

"What methods were used to obtain these sequences?"

));

240

wxStaticBoxSizer* itemStaticBoxSizer3 =

new

wxStaticBoxSizer(itemStaticBoxSizer3Static, wxVERTICAL);

241

itemBoxSizer2->Add(itemStaticBoxSizer3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

244

itemStaticBoxSizer3->Add(

m_MethodsSizer

, 0, wxALIGN_LEFT|wxALL, 0);

246

wxCheckBox* itemCheckBox5 =

new

wxCheckBox( itemPanel1,

ID_CHECKBOX5

(

"Sanger dideoxy sequencing"

), wxDefaultPosition, wxDefaultSize, 0 );

247

itemCheckBox5->SetValue(

false

);

250

wxCheckBox* itemCheckBox6 =

new

wxCheckBox( itemPanel1,

ID_CHECKBOX6

(

"454"

), wxDefaultPosition, wxDefaultSize, 0 );

251

itemCheckBox6->SetValue(

false

);

254

wxCheckBox* itemCheckBox7 =

new

wxCheckBox( itemPanel1,

ID_CHECKBOX7

(

"Helicos"

), wxDefaultPosition, wxDefaultSize, 0 );

255

itemCheckBox7->SetValue(

false

);

258

wxCheckBox* itemCheckBox8 =

new

wxCheckBox( itemPanel1,

ID_CHECKBOX8

(

"Illumina"

), wxDefaultPosition, wxDefaultSize, 0 );

259

itemCheckBox8->SetValue(

false

);

262

wxCheckBox* itemCheckBox9 =

new

wxCheckBox( itemPanel1,

ID_CHECKBOX9

(

"Ion Torrent"

), wxDefaultPosition, wxDefaultSize, 0 );

263

itemCheckBox9->SetValue(

false

);

266

wxCheckBox* itemCheckBox10 =

new

wxCheckBox( itemPanel1,

ID_CHECKBOX10

(

"Pacific Biosciences"

), wxDefaultPosition, wxDefaultSize, 0 );

267

itemCheckBox10->SetValue(

false

);

270

wxCheckBox* itemCheckBox11 =

new

wxCheckBox( itemPanel1,

ID_CHECKBOX11

(

"SOLiD"

), wxDefaultPosition, wxDefaultSize, 0 );

271

itemCheckBox11->SetValue(

false

);

274

wxBoxSizer* itemBoxSizer12 =

new

wxBoxSizer(wxHORIZONTAL);

275

itemStaticBoxSizer3->Add(itemBoxSizer12, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

279

itemBoxSizer12->Add(

m_OtherMethod

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

285

wxStaticBox* itemStaticBoxSizer15Static =

new

wxStaticBox(itemPanel1,

wxID_ANY

(

"What program(s) did you use to assemble your sequences?"

));

286

wxStaticBoxSizer* itemStaticBoxSizer15 =

new

wxStaticBoxSizer(itemStaticBoxSizer15Static, wxVERTICAL);

287

itemBoxSizer2->Add(itemStaticBoxSizer15, 0, wxGROW|wxALL, 5);

295 m_AddPrograms

new

wxHyperlinkCtrl( itemPanel1,

ID_BUTTON2

(

"Add More Assembly Programs"

), wxEmptyString, wxDefaultPosition, wxDefaultSize, wxHL_DEFAULT_STYLE );

298

wxFlexGridSizer* itemFlexGridSizer19 =

new

wxFlexGridSizer(2, 2, 0, 0);

299

itemBoxSizer2->Add(itemFlexGridSizer19, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

301

wxStaticText* itemStaticText20 =

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"Assembly Name (optional):"

), wxDefaultPosition, wxDefaultSize, 0 );

302

itemFlexGridSizer19->Add(itemStaticText20, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

305

itemFlexGridSizer19->Add(

m_AssemblyName

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

307

wxStaticText* itemStaticText22 =

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"Coverage (optional):"

), wxDefaultPosition, wxDefaultSize, 0 );

308

itemFlexGridSizer19->Add(itemStaticText22, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

311

itemFlexGridSizer19->Add(

m_Coverage

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

313

wxBoxSizer* itemBoxSizer23 =

new

wxBoxSizer(wxHORIZONTAL);

314

itemBoxSizer2->Add(itemBoxSizer23, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

316

wxHyperlinkCtrl* itemHyperlinkCtrl24 =

new

wxHyperlinkCtrl( itemPanel1,

ID_BUTTON

(

"Clear"

), wxEmptyString, wxDefaultPosition, wxDefaultSize, wxHL_DEFAULT_STYLE );

317

itemBoxSizer23->Add(itemHyperlinkCtrl24, 0, wxALL, 5);

329 while

(pos < itemList.size()) {

330

wxCheckBox* method_check =

dynamic_cast<

wxCheckBox*

>

(itemList[pos]->GetWindow());

332

method_check->SetValue(

false

);

368 if

(!wxPanel::TransferDataToWindow())

374 string

field_name =

""

;

375 const CObject_id

& obj_id = (*it)->GetLabel();

376 if

( obj_id.

IsStr

() ) {

377

field_name = obj_id.

GetStr

();

380 if

((*it)->IsSetData()) {

381 if

((*it)->GetData().IsStr()) {

382 value

= (*it)->GetData().GetStr();

383

}

else if

((*it)->GetData().IsInt()) {

398

vector<string> techs;

400 string

other_methods =

""

;

401 ITERATE

(vector<string>, it, techs) {

406 while

(pos < itemList.size() && !found) {

407

wxCheckBox* method_check =

dynamic_cast<

wxCheckBox*

>

(itemList[pos]->GetWindow());

410

method_check->SetValue(

true

);

418

other_methods +=

"; "

;

420

other_methods += *it;

439 "Sequencing Technology"

440 "StructuredCommentPrefix"

441 "StructuredCommentSuffix" 448 if

label

.IsStr()) {

462 if

(!wxPanel::TransferDataFromWindow())

465

CUser_object::TData::iterator it =

m_User

->SetData().begin();

466 while

(it !=

m_User

->SetData().end()) {

468

it =

m_User

->SetData().erase(it);

480 m_User

->AddField (

"StructuredCommentPrefix"

, prefix);

503 while

(pos < itemList.size()) {

504

wxCheckBox* method_check =

dynamic_cast<

wxCheckBox*

>

(itemList[pos]->GetWindow());

506 if

(method_check->GetValue()) {

521

method += other_method;

525

seqtech.

SetData

().SetStr(method);

529 m_User

->AddField (

"StructuredCommentSuffix"

, prefix);

618 m_User

->Assign(desc.GetUser());

User-defined methods of the data storage class.

EVT_CHECKBOX(ID_CADJUSTFEATURES_CHECKBOX, CAdjustFeaturesForGaps::OnKnownUnknownSelected) EVT_CHECKBOX(ID_CADJUSTFEATURES_CHECKBOX1

virtual string GetValue()

virtual void SetValue(const string &val)

CRegistryWriteView GetWriteView(const string &section)

get a read-write view at a particular level.

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

class CRegistryReadView provides a nested hierarchical view at a particular key.

bool GetBool(const string &key, bool default_val=false) const

void Set(const string &key, int val)

access a named key at this level, with no recursion

wxHyperlinkCtrl * m_AddPrograms

virtual bool TransferDataFromWindow()

wxBoxSizer * m_MethodsSizer

void x_ChangeToMultiplePrograms()

CRef< objects::CUser_object > GetUser_object() const

CRef< objects::CUser_object > m_User

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

Creation.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

CSingleAssemblyProgramPanel * m_SingleAssemblyProgram

~CSequencingTechnologyPanel()

Destructor.

wxChoice * m_StandardCommentCtrl

void CreateControls()

Creates the controls and sizers.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void SaveSettings() const

static bool ShowToolTips()

Should we show tooltips?

void SetRegistryPath(const string &reg_path)

wxTextCtrl * m_AssemblyName

virtual void UpdateSeqdesc(objects::CSeqdesc &desc)

virtual bool TransferDataToWindow()

void Init()

Initialises member variables.

wxTextCtrl * m_OtherMethodText

wxCheckBox * m_OtherMethod

virtual void ChangeSeqdesc(const objects::CSeqdesc &desc)

void OnOtherMethodClick(wxCommandEvent &event)

wxEVT_COMMAND_CHECKBOX_CLICKED event handler for ID_CHECKBOX12

void OnButton2HyperlinkClicked(wxHyperlinkEvent &event)

wxEVT_COMMAND_HYPERLINK event handler for ID_BUTTON2

CSequencingTechnologyPanel()

Constructors.

void OnClearClicked(wxHyperlinkEvent &event)

wxEVT_COMMAND_HYPERLINK event handler for ID_BUTTON

wxBoxSizer * m_AssemblyProgramSizer

CAssemblyProgramPanel * m_AssemblyProgram

virtual string GetValue()

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

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

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

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.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

static const char label[]

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

void SetData(TData &value)

Assign a value to Data data member.

vector< CRef< CUser_field > > TData

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

const GenericPointer< typename T::ValueType > T2 value

static const int kNumKnownFields

static bool IsKnownField(const CObject_id &label)

static const char * kReplaceAll

static const string kKnownFields[]

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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