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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/rawseqtodeltabyn__panel_8cpp_source.html below:

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

36 #include <wx/radiobut.h> 37 #include <wx/textctrl.h> 38 #include <wx/checkbox.h> 39 #include <wx/stattext.h> 40 #include <wx/choice.h> 41 #include <wx/statbox.h> 86 bool

keep_gap_length,

bool

hide_linkage_info,

87

wxWindowID

id

const

wxPoint& pos,

const

wxSize&

size

long

style )

88

: m_AdjustCDSValue(adjust_cds),

89

m_AddLinkageValue(add_linkage),

90

m_KeepGapLengthValue(keep_gap_length),

91

m_HideLinkageInfo(hide_linkage_info)

105

wxPanel::Create( parent,

id

, pos,

size

, style );

110

GetSizer()->SetSizeHints(

this

);

160

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

161

itemPanel1->SetSizer(itemBoxSizer2);

163

wxStaticText* itemStaticText3 =

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"Choose length of Ns to convert to gaps of unknown length"

), wxDefaultPosition, wxDefaultSize, 0 );

164

itemBoxSizer2->Add(itemStaticText3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

166

wxBoxSizer* itemBoxSizer4 =

new

wxBoxSizer(wxHORIZONTAL);

167

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

169

wxBoxSizer* itemBoxSizer5 =

new

wxBoxSizer(wxVERTICAL);

170

itemBoxSizer4->Add(itemBoxSizer5, 0, wxALIGN_CENTER_VERTICAL|wxALL, 0);

178

wxRadioButton* itemRadioButton7 =

new

wxRadioButton( itemPanel1,

ID_RAW_SEQ_TO_DELTA_BY_N_RB2

(

">="

), wxDefaultPosition, wxDefaultSize, 0 );

179

itemRadioButton7->SetValue(

false

);

180

itemBoxSizer5->Add(itemRadioButton7, 0, wxALIGN_LEFT|wxALL, 5);

186 m_KeepGapLength

new

wxCheckBox( itemPanel1,

ID_CHECKBOX

(

"Do not adjust gap length in sequence to 100 N's"

), wxDefaultPosition, wxDefaultSize, 0 );

188

itemBoxSizer2->Add(

m_KeepGapLength

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

190

wxStaticText* itemStaticText9 =

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"Choose length of Ns to convert to gaps of known length"

), wxDefaultPosition, wxDefaultSize, 0 );

191

itemBoxSizer2->Add(itemStaticText9, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

193

wxBoxSizer* itemBoxSizer10 =

new

wxBoxSizer(wxHORIZONTAL);

194

itemBoxSizer2->Add(itemBoxSizer10, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

196

wxBoxSizer* itemBoxSizer11 =

new

wxBoxSizer(wxVERTICAL);

197

itemBoxSizer10->Add(itemBoxSizer11, 0, wxALIGN_CENTER_VERTICAL|wxALL, 0);

203

wxRadioButton* itemRadioButton13 =

new

wxRadioButton( itemPanel1,

ID_RAW_SEQ_TO_DELTA_BY_N_RB4

(

">="

), wxDefaultPosition, wxDefaultSize, 0 );

204

itemRadioButton13->SetValue(

true

);

205

itemBoxSizer11->Add(itemRadioButton13, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

208

itemBoxSizer10->Add(

m_TextCtrl_known

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

210

wxStaticBox* itemStaticBoxSizer15Static =

new

wxStaticBox(itemPanel1,

wxID_ANY

, wxEmptyString);

211

wxStaticBoxSizer* itemStaticBoxSizer15 =

new

wxStaticBoxSizer(itemStaticBoxSizer15Static, wxHORIZONTAL);

212

itemBoxSizer2->Add(itemStaticBoxSizer15, 1, wxGROW|wxALL, 2);

214 m_Description

new

wxStaticText( itemPanel1, wxID_STATIC, wxEmptyString, wxDefaultPosition, wxSize(-1, 50), 0 );

215

itemStaticBoxSizer15->Add(

m_Description

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

218 m_AdjustCDS

new

wxCheckBox( itemPanel1,

ID_CHECKBOX

(

"Adjust CDS locations for gaps"

), wxDefaultPosition, wxDefaultSize, 0 );

220

itemBoxSizer2->Add(

m_AdjustCDS

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

224

itemBoxSizer2->Add(

m_AddLinkage

, 0, wxALIGN_LEFT|wxALL, 5);

234

wxArrayString type_str, linkage_str, linkage_evidence_str;

235

type_str.Add(

"within"

);

236

type_str.Add(

"between"

);

237 for

(CEnumeratedTypeValues::TValues::const_iterator

= type_values.begin();

!= type_values.end(); ++

)

239

type_str.Add(wxString(

->first));

242

linkage_str.Add(

(

"Within Scaffolds"

));

243

linkage_str.Add(

(

"Between Scaffolds"

));

245 for

(CEnumeratedTypeValues::TValues::const_iterator

= linkage_evidence_values.begin();

!= linkage_evidence_values.end(); ++

)

247

linkage_evidence_str.Add(wxString(

->first));

250

wxFlexGridSizer* itemFlexGridSizer19 =

new

wxFlexGridSizer(0, 2, 0, 0);

251

itemBoxSizer2->Add(itemFlexGridSizer19, 0, wxALIGN_CENTER_HORIZONTAL | wxALL, 2);

253

wxStaticText* itemStaticText20 =

new

wxStaticText(itemPanel1, wxID_STATIC,

(

"Gap Type"

), wxDefaultPosition, wxDefaultSize, 0);

254

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

257

itemFlexGridSizer19->Add(

m_GapType

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

261

wxStaticText* itemStaticText22 =

new

wxStaticText(itemPanel1, wxID_STATIC,

(

"Linkage"

), wxDefaultPosition, wxDefaultSize, 0);

262

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

265

itemFlexGridSizer19->Add(

m_Linkage

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

269

wxStaticText* itemStaticText24 =

new

wxStaticText(itemPanel1, wxID_STATIC,

(

"Linkage Evidence"

), wxDefaultPosition, wxDefaultSize, 0);

270

itemFlexGridSizer19->Add(itemStaticText24, 0, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL | wxALL, 5);

273

itemFlexGridSizer19->Add(

m_LinkageEvidence

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

329

min_unknown = INT_MAX;

335

max_known = min_known;

340

max_unknown = min_unknown;

349 if

(min_unknown != INT_MAX) {

355 if

(min_known != INT_MAX) {

364 if

(max_unknown != min_unknown) {

367

rdbtn->SetValue(

true

);

395

is_assembly_gap =

false

;

398

linkage_evidence = -1;

405 int

gap_type_sel =

m_GapType

->GetSelection();

406 int

linkage_sel =

m_Linkage

->GetSelection();

409 if

(gap_type_sel != wxNOT_FOUND)

411 string

gap_type_str =

m_GapType

->GetString(gap_type_sel).ToStdString();

412 if

(gap_type_str ==

"within"

)

413

gap_type_str =

"scaffold"

;

414 if

(gap_type_str ==

"between"

)

415

gap_type_str =

"contig"

;

418 if

(gap_type_str ==

"repeat"

)

420 if

(linkage_sel != wxNOT_FOUND)

422 if

(

m_Linkage

->GetString(linkage_sel) ==

(

"Within Scaffolds"

))

429 if

(gap_type_str ==

"scaffold"

)

434 if

(gap_type_str ==

"contamination"

)

446 int

linkage_val = -1;

447 int

linkage_evidence_val = -1;

448 GetAssemblyParams

(is_assembly_gap, gap_type_val, linkage_val, linkage_evidence_val);

450

gap_type = linkage = linkage_evidence =

kEmptyStr

;

454 if

(is_assembly_gap) {

455 int

gap_type_sel =

m_GapType

->GetSelection();

456

gap_type =

m_GapType

->GetString(gap_type_sel).ToStdString();

458 if

(linkage_val > -1) {

459 int

linkage_sel =

m_Linkage

->GetSelection();

460

linkage =

m_Linkage

->GetString(linkage_sel).ToStdString();

463 if

(linkage_evidence_val > -1) {

465

linkage_evidence =

m_LinkageEvidence

->GetString(linkage_evidence_sel).ToStdString();

473 string

gap_type_sel = gap_type;

475

gap_type_sel =

"within"

;

478

gap_type_sel =

"between"

;

482 if

(linkage ==

"linked"

) {

485 else if

(linkage ==

"unlinked"

) {

489 if

(gap_type ==

"repeat"

) {

493 if

(!linkage_evidence.empty()) {

513 long

min_known = INT_MAX;

515 long

min_unknown = INT_MAX;

517 GetMinMax

(min_known, max_known, min_unknown, max_unknown);

519 if

(min_unknown < INT_MAX)

521 if

(min_unknown == max_unknown)

522 text

(

" All sequences of exactly "

) << min_unknown <<

(

" Ns will be converted to gaps of unknown length."

);

524 text

(

" All sequences of Ns with lengths >= "

) << min_unknown <<

(

" will be converted to gaps of unknown length."

);

526 if

(min_known < INT_MAX)

528 if

(min_known == max_known)

529 text

(

" All sequences of exactly "

) << min_known <<

(

" Ns will be converted to gaps of known length."

);

531 text

(

" All sequences of Ns with lengths >= "

) << min_known <<

(

" will be converted to gaps of known length."

);

556 int

gap_type =

m_GapType

->GetSelection();

557 if

(gap_type != wxNOT_FOUND)

559 auto

gap_str =

m_GapType

->GetString(gap_type);

561 if

(gap_str ==

(

"repeat"

))

566 if

(gap_str ==

(

"scaffold"

) || gap_str ==

(

"within"

))

589 int

gap_type =

m_GapType

->GetSelection();

590 int

linkage =

m_Linkage

->GetSelection();

591 if

(gap_type != wxNOT_FOUND)

593 auto

gap_str =

m_GapType

->GetString(gap_type);

594 if

(gap_str ==

(

"repeat"

))

597 if

(linkage != wxNOT_FOUND &&

m_Linkage

->GetString(linkage) ==

(

"Within Scaffolds"

))

602 if

(gap_str ==

(

"scaffold"

) || gap_str ==

(

"within"

))

606 if

(gap_str ==

(

"contamination"

)) {

623 int

gap_type =

m_GapType

->GetSelection();

624 int

linkage =

m_Linkage

->GetSelection();

625 if

(gap_type != wxNOT_FOUND &&

m_GapType

->GetString(gap_type) ==

(

"repeat"

) &&

626

linkage != wxNOT_FOUND &&

m_Linkage

->GetString(linkage) ==

(

"Within Scaffolds"

))

User-defined methods of the data storage class.

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

bool m_KeepGapLengthValue

wxRadioButton * m_RadioButton_known

void Init()

Initialises member variables.

void OnAddLinkage(wxCommandEvent &event)

wxEVT_COMMAND_CHECKBOX_CLICKED event handler for ID_RAW_SEQ_TO_DELTA_BY_N_ADD_LINKAGE

wxRadioButton * m_RadioButton_unknown

wxTextCtrl * m_TextCtrl_unknown

void SetKeepGapLength(bool value)

void OnLinkage(wxCommandEvent &event)

wxEVT_COMMAND_CHOICE_SELECTED event handler for ID_RAW_SEQ_TO_DELTA_BY_N_LINKAGE

wxChoice * m_LinkageEvidence

void GetExplanation(wxCommandEvent &event)

wxEVT_COMMAND_RADIOBUTTON_SELECTED event handler for ID_RAW_SEQ_TO_DELTA_BY_N_RB1

void CreateControls()

Creates the controls and sizers.

bool GetAdjustCDS() const

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

Creation.

wxStaticText * m_Description

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void OnGapType(wxCommandEvent &event)

wxEVT_COMMAND_CHOICE_SELECTED event handler for ID_RAW_SEQ_TO_DELTA_BY_N_GAP_TYPE

void GetMinMax(long &min_known, long &max_known, long &min_unknown, long &max_unknown)

void SetAssemblyParams(bool is_assembly_gap, const string &gap_type, const string &linkage, const string &linkage_evidence)

bool GetKeepGapLength() const

void SetMinMax(const long min_known, const long max_known, const long min_unknown, const long max_unknown)

CRawSeqToDeltaByNPanel()

Constructors.

@ ID_RAW_SEQ_TO_DELTA_BY_N_ADD_LINKAGE

@ ID_RAW_SEQ_TO_DELTA_BY_N_RB4

@ ID_RAW_SEQ_TO_DELTA_BY_N_RB2

@ ID_RAW_SEQ_TO_DELTA_BY_N_LINKAGE

@ ID_RAW_SEQ_TO_DELTA_BY_N_RB1

@ ID_RAW_SEQ_TO_DELTA_BY_N_GAP_TYPE

@ ID_RAW_SEQ_TO_DELTA_BY_N_LINKEVIDENCE

@ ID_RAW_SEQ_TO_DELTA_BY_N_TC2

@ ID_RAW_SEQ_TO_DELTA_BY_N_RB3

@ ID_RAW_SEQ_TO_DELTA_BY_N_TC1

~CRawSeqToDeltaByNPanel()

Destructor.

wxTextCtrl * m_TextCtrl_known

wxCheckBox * m_KeepGapLength

void SetAdjustCDS(bool value)

static bool ShowToolTips()

Should we show tooltips?

void GetAssemblyParams(bool &is_assembly_gap, int &gap_type, int &linkage, int &linkage_evidence)

wxCheckBox * m_AddLinkage

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

list< pair< string, TEnumValueType > > TValues

#define ENUM_METHOD_NAME(EnumName)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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 enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static void text(MDB_val *v)

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

const GenericPointer< typename T::ValueType > T2 value

wxString ToWxString(const string &s)

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