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

46 #include <wx/stattext.h> 47 #include <wx/statbox.h> 48 #include <wx/textctrl.h> 49 #include <wx/button.h> 50 #include <wx/scrolwin.h> 51 #include <wx/bitmap.h> 52 #include <wx/checkbox.h> 54 #include <wx/choice.h> 55 #include <wx/radiobox.h> 98  Create

(parent,

id

, caption, pos,

size

, style);

109 

CAlgoToolManagerParamsPanel::Create( parent,

id

, pos,

size

, style );

114

GetSizer()->SetSizeHints(

this

);

181  if

(all_present && all_unique)

183

status =

"All present, all unique"

;

185  else if

(all_present && is_unique)

187

status =

"All present, one unique"

;

189  else if

(all_present && ! is_unique)

191

status =

"All present, mixed"

;

193  else if

(! all_present && all_unique)

195

status =

"Some missing, all unique"

;

197  else if

(! all_present && is_unique)

199

status =

"Some missing, one unique"

;

201  else if

(! all_present && ! is_unique)

203

status =

"Some missing, mixed"

;

218

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

219

itemDialog1->SetSizer(itemBoxSizer2);

224

wxStaticBox* itemStaticBoxSizer4Static =

new

wxStaticBox(itemDialog1,

wxID_ANY

,

_

(

"Organism Description"

));

225

wxStaticBoxSizer* itemStaticBoxSizer4 =

new

wxStaticBoxSizer(itemStaticBoxSizer4Static, wxVERTICAL);

226

itemBoxSizer2->Add(itemStaticBoxSizer4, 0, wxGROW|wxALL, 5);

228

wxBoxSizer* modifierLimitsSizer =

new

wxBoxSizer (wxHORIZONTAL);

229

itemStaticBoxSizer4->Add (modifierLimitsSizer, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

231

wxStaticText* itemStaticText7 =

new

wxStaticText( itemDialog1, wxID_STATIC,

_

(

"Modifier List"

), wxDefaultPosition, wxDefaultSize, 0 );

232

modifierLimitsSizer->Add(itemStaticText7, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

234

wxArrayString m_ModifierListChoiceStrings;

235

m_ModifierListChoiceStrings.Add(

_

(

"Custom"

));

236

m_ModifierListChoiceStrings.Add(

_

(

"All"

));

241

wxStaticText* itemStaticText10 =

new

wxStaticText( itemDialog1, wxID_STATIC,

_

(

"Maximum modifiers per line"

), wxDefaultPosition, wxDefaultSize, 0 );

242

modifierLimitsSizer->Add(itemStaticText10, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

244

wxArrayString m_MaxModifiersStrings;

246

m_MaxModifiersStrings.Add(

_

(

"no limit"

));

248  int

num_total_mods = 0;

252

m_MaxModifiersStrings.Add

258

wxDefaultPosition, wxDefaultSize,

259

m_MaxModifiersStrings, 0 );

261

wxALIGN_CENTER_VERTICAL|wxALL, 5);

266  _

(

"Use labels (e.g., 'strain BALB')"

),

267

wxDefaultPosition, wxDefaultSize, 0 );

270

wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

272

wxStaticBox* modifierGroupLabelBox =

273  new

wxStaticBox( itemDialog1, wxID_STATIC,

_

(

"Available Modifiers"

),

274

wxDefaultPosition, wxDefaultSize, 0 );

275

wxStaticBoxSizer* modifierGroup =

276  new

wxStaticBoxSizer(modifierGroupLabelBox, wxHORIZONTAL);

277

itemStaticBoxSizer4->Add(modifierGroup, 0, wxGROW|wxALL, 5);

279

wxBoxSizer* modifierColumn =

new

wxBoxSizer (wxVERTICAL);

280

modifierGroup->Add(modifierColumn, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

281  int

num_in_column = 0;

284  if

(num_in_column == 4) {

285

modifierColumn =

new

wxBoxSizer (wxVERTICAL);

286

modifierGroup->Add(modifierColumn, 0,

287

wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

290

wxBoxSizer *

row

=

new

wxBoxSizer (wxHORIZONTAL);

291

modifierColumn->Add (

row

, 0, wxALIGN_LEFT|wxALL, 5);

295

wxDefaultPosition, wxDefaultSize, 0 ));

303  if

(first_value.length() > 25) {

304

first_value = first_value.substr(0, 22) +

"..."

;

306  label

+=

" '"

+ first_value +

"'"

;

307

wxStaticText* textLabel =

308  new

wxStaticText( itemDialog1, wxID_STATIC,

310

wxDefaultPosition, wxDefaultSize, 0 );

311  row

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

320

wxArrayString HIVStrings;

321

HIVStrings.Add(

_

(

"Prefer Clone"

));

322

HIVStrings.Add(

_

(

"Prefer Isolate"

));

323

HIVStrings.Add(

_

(

"Want Both Isolate and Clone"

));

325  m_HIVRule

=

new

wxRadioBox (itemDialog1,

wxID_ANY

,

_

(

"HIV Rule"

), wxDefaultPosition, wxDefaultSize,

326

HIVStrings, 1, wxRA_SPECIFY_ROWS);

327

itemStaticBoxSizer4->Add (

m_HIVRule

, 0, wxALIGN_LEFT|wxALL, 5);

330

wxStaticBox* otherOptionsGroupLabelBox =

new

wxStaticBox( itemDialog1, wxID_STATIC,

_

(

"Other Options"

), wxDefaultPosition, wxDefaultSize, 0 );

331

wxStaticBoxSizer* otherOptionsGroup =

new

wxStaticBoxSizer(otherOptionsGroupLabelBox, wxHORIZONTAL);

332

itemStaticBoxSizer4->Add(otherOptionsGroup, 0, wxGROW|wxALL, 5);

334

wxBoxSizer* otherOptionsColumn =

new

wxBoxSizer (wxVERTICAL);

335

otherOptionsGroup->Add(otherOptionsColumn, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

339

otherOptionsColumn->Add(

m_LeaveParen

, 0, wxALIGN_LEFT|wxALL, 5);

341  m_NoSp

=

new

wxCheckBox( itemDialog1,

ID_DO_NOT_APPLY_TO_SP

,

_

(

"Do not apply modifiers to 'sp.' organisms"

), wxDefaultPosition, wxDefaultSize, 0 );

342  m_NoSp

->SetValue(

true

);

343

otherOptionsColumn->Add(

m_NoSp

, 0, wxALIGN_LEFT|wxALL, 5);

345  m_NoNr

=

new

wxCheckBox( itemDialog1,

ID_DO_NOT_APPLY_TO_NR

,

_

(

"Do not apply modifiers to 'nr.' organisms"

), wxDefaultPosition, wxDefaultSize, 0 );

346  m_NoNr

->SetValue(

true

);

347

otherOptionsColumn->Add(

m_NoNr

, 0, wxALIGN_LEFT|wxALL, 5);

349

otherOptionsColumn =

new

wxBoxSizer (wxVERTICAL);

350

otherOptionsGroup->Add(otherOptionsColumn, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

356  m_NoCf

=

new

wxCheckBox( itemDialog1,

ID_DO_NOT_APPLY_TO_CF

,

_

(

"Do not apply modifiers to 'cf.' organisms"

), wxDefaultPosition, wxDefaultSize, 0 );

357  m_NoCf

->SetValue(

true

);

358

otherOptionsColumn->Add(

m_NoCf

, 0, wxALIGN_LEFT|wxALL, 5);

360  m_NoAff

=

new

wxCheckBox( itemDialog1,

ID_DO_NOT_APPLY_TO_AFF

,

_

(

"Do not apply modifiers to 'aff.' organisms"

), wxDefaultPosition, wxDefaultSize, 0 );

362

otherOptionsColumn->Add(

m_NoAff

, 0, wxALIGN_LEFT|wxALL, 5);

364

otherOptionsColumn =

new

wxBoxSizer (wxVERTICAL);

365

otherOptionsGroup->Add(otherOptionsColumn, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

371

wxStaticBox* itemStaticBoxSizer17Static =

new

wxStaticBox(itemDialog1,

wxID_ANY

,

_

(

"Feature Clauses"

));

372

wxStaticBoxSizer* featureBox =

new

wxStaticBoxSizer(itemStaticBoxSizer17Static, wxVERTICAL);

373

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

375

wxBoxSizer* featureRow1 =

new

wxBoxSizer (wxHORIZONTAL);

376

featureBox->Add (featureRow1, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

378

wxBoxSizer* featureListGroup =

new

wxBoxSizer (wxVERTICAL);

379

featureRow1->Add (featureListGroup, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

381

wxBoxSizer* itemBoxSizer18 =

new

wxBoxSizer(wxHORIZONTAL);

382

featureListGroup->Add(itemBoxSizer18, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

384

wxStaticText* itemStaticText19 =

new

wxStaticText( itemDialog1, wxID_STATIC,

_

(

"Features or Complete"

), wxDefaultPosition, wxDefaultSize, 0 );

385

itemBoxSizer18->Add(itemStaticText19, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

387

wxArrayString m_FeatureListChoiceStrings;

388

m_FeatureListChoiceStrings.Add(

_

(

"List Features"

));

389

m_FeatureListChoiceStrings.Add(

_

(

"Complete Sequence"

));

390

m_FeatureListChoiceStrings.Add(

_

(

"Complete Genome"

));

395

wxArrayString m_ProductClauseChoiceStrings;

396

m_ProductClauseChoiceStrings.Add(

_

(

"No mitochondrial or chloroplast suffix"

));

397

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear gene(s) for mitochondrial product(s)"

));

398

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear gene(s) for chloroplast product(s)"

));

399

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear gene(s) for kinetoplast product(s)"

));

400

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear gene(s) for plastid product(s)"

));

401

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear gene(s) for chromoplast product(s)"

));

402

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear gene(s) for cyanelle product(s)"

));

403

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear gene(s) for apicoplast product(s)"

));

404

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear gene(s) for leucoplast product(s)"

));

405

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear gene(s) for proplastid product(s)"

));

406

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear genes based on CDS products"

));

407

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear copy of mitochondrial gene"

));

408

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear copy of chloroplast gene"

));

409

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear copy of kinetoplast gene"

));

410

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear copy of plastid gene"

));

411

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear copy of chromoplast gene"

));

412

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear copy of cyanelle gene"

));

413

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear copy of apicoplast gene"

));

414

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear copy of leucoplast gene"

));

415

m_ProductClauseChoiceStrings.Add(

_

(

"Nuclear copy of proplastid gene"

));

428

wxStaticBox* optionalFeaturesBoxLabel =

new

wxStaticBox(itemDialog1,

wxID_ANY

,

_

(

"Optional Features"

));

429

wxStaticBoxSizer* optionalFeaturesBox =

new

wxStaticBoxSizer(optionalFeaturesBoxLabel, wxHORIZONTAL);

430

featureRow1->Add(optionalFeaturesBox, 0, wxGROW|wxALL, 5);

432

wxBoxSizer* optionalFeaturesColumn =

new

wxBoxSizer (wxVERTICAL);

433

optionalFeaturesBox->Add (optionalFeaturesColumn, 0, wxALIGN_LEFT|wxALL, 5);

437

optionalFeaturesColumn->Add(

m_KeepExons

, 0, wxALIGN_LEFT|wxALL, 5);

441

optionalFeaturesColumn->Add(

m_KeepIntrons

, 0, wxALIGN_LEFT|wxALL, 5);

445

optionalFeaturesColumn->Add(

m_Keep5UTRs

, 0, wxALIGN_LEFT|wxALL, 5);

449

optionalFeaturesColumn->Add(

m_Keep3UTRs

, 0, wxALIGN_LEFT|wxALL, 5);

451

optionalFeaturesColumn =

new

wxBoxSizer (wxVERTICAL);

452

optionalFeaturesBox->Add (optionalFeaturesColumn, 0, wxALIGN_LEFT|wxALL, 5);

461

optionalFeaturesColumn =

new

wxBoxSizer (wxVERTICAL);

462

optionalFeaturesBox->Add (optionalFeaturesColumn, 0, wxALIGN_LEFT|wxALL, 5);

466

optionalFeaturesColumn->Add(

m_KeepMiscFeats

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

468

wxArrayString m_MiscFeatParseRuleStrings;

469

m_MiscFeatParseRuleStrings.Add(

_

(

"Look for Noncoding Products"

));

470

m_MiscFeatParseRuleStrings.Add(

_

(

"Use comment before first semicolon"

));

476

wxBoxSizer* featureRow2 =

new

wxBoxSizer (wxHORIZONTAL);

477

featureBox->Add (featureRow2, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

479

wxStaticBox* suppressFeaturesBoxLabel =

new

wxStaticBox(itemDialog1,

wxID_ANY

,

_

(

"Suppress Features"

));

480

wxStaticBoxSizer* suppressFeaturesBox =

new

wxStaticBoxSizer(suppressFeaturesBoxLabel, wxHORIZONTAL);

481

featureRow2->Add(suppressFeaturesBox, 0, wxGROW|wxALL, 5);

483

wxButton* itemButton39 =

new

wxButton( itemDialog1,

ID_SUPPRESS_FEATURES

,

_

(

"Suppress Features"

), wxDefaultPosition, wxDefaultSize, 0 );

484

suppressFeaturesBox->Add(itemButton39, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

486

wxStaticBox* suppressOptionsBoxLabel =

new

wxStaticBox(itemDialog1,

wxID_ANY

,

_

(

"Suppress"

));

487

wxStaticBoxSizer* suppressOptionsBox =

new

wxStaticBoxSizer(suppressOptionsBoxLabel, wxVERTICAL);

488

featureRow2->Add(suppressOptionsBox, 0, wxGROW|wxALL, 5);

685  return

wxPanel::TransferDataToWindow();

691  if

(wxPanel::TransferDataFromWindow()) {

742  if

(selected == 10) {

780  else if

(selected > 10) {

900  bool

allow_hiv_rule =

true

;

903  n

<

m_ModifierButtons

.size() && n < m_Params->m_ModifierList.size() && allow_hiv_rule;

911

allow_hiv_rule =

false

;

914  return

allow_hiv_rule;

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

static string s_GetModifierStatus(bool all_present, bool all_unique, bool is_unique)

static const char * kTableTag

#define ID_SUPPRESS_GENE_CLUSTER

#define ID_INCLUDE_INTRONS

#define ID_MODIFIERS_PER_LINE

#define ID_INCLUDE_MISC_FEATS

#define ID_SUPPRESS_ALTERNATIVE_SPLICE

#define ID_MODIFIER_CHECKBOX

#define ID_SUPPRESS_TRANSPOSON

#define ID_INCLUDE_REGULATORY_FEATURES

#define ID_USE_FAKE_PROMOTERS

#define ID_LEAVE_PARENTHETICAL

#define ID_INCLUDE_COUNTRY_TEXT

#define ID_USE_NCRNA_COMMENT

#define ID_SUPPRESS_LOCUS_TAGS

#define ID_DO_NOT_APPLY_TO_AFF

#define ID_SUPPRESS_FEATURES

#define ID_DO_NOT_APPLY_TO_SP

#define ID_ADD_ALT_SPLICE

#define ID_KEEP_AFTER_SEMICOLON

#define ID_MISC_FEAT_RULE

#define ID_DO_NOT_APPLY_TO_CF

#define ID_DO_NOT_APPLY_TO_NR

void OnChangeMiscFeat(wxCommandEvent &event)

bool Create(wxWindow *parent, wxWindowID id=10025, const wxString &caption=_("Autodef Params Panel"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

wxCheckBox * m_IncludeCountry

void Init()

Initializes member variables.

vector< wxCheckBox * > m_ModifierButtons

wxChoice * m_MaxModifiers

wxChoice * m_FeatureListChoice

bool TransferDataFromWindow()

static bool ShowToolTips()

Should we show tooltips?

set< objects::CFeatListItem > m_SuppressedFeatures

wxChoice * m_ModifierListChoice

void RestoreDefaults()

override in derived classes

void SetParams(SAutodefParams *params, TConstScopedObjects *objects)

void OnChangeModifierListChoice(wxCommandEvent &event)

wxCheckBox * m_SuppressTransposon

wxCheckBox * m_AppendAltSplice

void CreateControls()

Creates the controls and sizers.

virtual void SetRegistryPath(const string &path)

CAlgoToolManagerParamsPanel.

virtual void LoadSettings()

wxChoice * m_ProductClauseChoice

wxCheckBox * m_LeaveParen

wxCheckBox * m_SuppressAltSplice

wxChoice * m_MiscFeatParseRule

wxCheckBox * m_KeepMiscFeats

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

wxCheckBox * m_SuppressLocusTags

wxCheckBox * m_KeepRegulatoryFeatures

wxCheckBox * m_UseFakePromoters

wxCheckBox * m_KeepAfterSemicolon

void OnChangeModifierSelection(wxCommandEvent &event)

wxCheckBox * m_KeepIntrons

wxCheckBox * m_SupressGeneCluster

wxCheckBox * m_UseNcRNAComment

void OnSuppressFeatures(wxCommandEvent &event)

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

~CAutodefParamsPanel()

Destructor.

bool TransferDataToWindow()

TConstScopedObjects * m_InputObjects

virtual void SaveSettings() const

override in derived classes

SAutodefParams * m_Params

CObjectListWidget * m_ObjectListCtrl

CAutodefParamsPanel()

Constructors.

void GetSelected(TFeatTypeItemSet &feat_types)

void SetSelected(TFeatTypeItemSet &feat_types)

static string MakeKey(const string &section, const string &key, const string &delim=CGuiRegistry::kDecimalDot)

create a key from a section and a subkey

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.

set< objects::CFeatListItem > m_SuppressedFeatures

bool m_SuppressMobileElementSubfeatures

unsigned int m_MiscFeatRule

objects::CAutoDefSourceDescription::TAvailableModifierVector m_ModifierList

bool m_LeaveParenthetical

bool m_KeepRegulatoryFeatures

bool m_KeepAfterSemicolon

bool m_SuppressFeatureAltSplice

unsigned int m_ProductFlag

unsigned int m_NuclearCopyFlag

unsigned int m_FeatureListType

bool m_IncludeCountryText

bool m_SpecifyNuclearProduct

bool m_GeneClusterOppStrand

TConstScopedObjects m_SeqEntries

vector< SConstScopedObject > TConstScopedObjects

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert int to string.

static const char label[]

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

#define row(bind, expected)

wxString ToWxString(const string &s)

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