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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/subprepintropanel_8cpp_source.html below:

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

49 #include <wx/msgdlg.h> 92

m_Workbench(workbench)

106

wxPanel::Create( parent,

id

, pos,

size

, style );

111

GetSizer()->SetSizeHints(

this

);

157

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

158

itemPanel1->SetSizer(itemBoxSizer2);

160

wxFlexGridSizer* itemFlexGridSizer3 =

new

wxFlexGridSizer(0, 4, 0, 0);

161

itemBoxSizer2->Add(itemFlexGridSizer3, 0, wxALIGN_LEFT|wxALL, 5);

163

wxStaticText* itemStaticText4 =

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"Submission Information"

), wxDefaultPosition, wxSize(100, -1), wxALIGN_CENTRE );

164

itemStaticText4->Wrap(20);

165

itemFlexGridSizer3->Add(itemStaticText4, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

167 m_StarSubmitter

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"*"

), wxDefaultPosition, wxDefaultSize, 0 );

169 m_StarSubmitter

->SetFont(wxFont(12, wxFONTFAMILY_SWISS, wxFONTSTYLE_NORMAL, wxFONTWEIGHT_NORMAL,

false

wxT

(

"Tahoma"

)));

170

itemFlexGridSizer3->Add(

m_StarSubmitter

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

172 m_SubmitterLabel

new

wxTextCtrl( itemPanel1, wxID_STATIC, wxEmptyString, wxDefaultPosition, wxSize(400, -1), wxTE_MULTILINE|wxTE_READONLY );

173

itemFlexGridSizer3->Add(

m_SubmitterLabel

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

175

wxHyperlinkCtrl* itemHyperlinkCtrl7 =

new

wxHyperlinkCtrl( itemPanel1,

ID_HYPERLINKCTRL5

(

"Edit"

), wxEmptyString, wxDefaultPosition, wxSize(20, -1), wxHL_DEFAULT_STYLE );

176

itemFlexGridSizer3->Add(itemHyperlinkCtrl7, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

178

wxStaticText* itemStaticText8 =

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"Submission Type"

), wxDefaultPosition, wxDefaultSize, wxALIGN_CENTRE );

179

itemFlexGridSizer3->Add(itemStaticText8, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

181 m_StarType

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"*"

), wxDefaultPosition, wxDefaultSize, 0 );

182 m_StarType

->SetForegroundColour(wxColour(255, 0, 0));

183 m_StarType

->SetFont(wxFont(12, wxFONTFAMILY_SWISS, wxFONTSTYLE_NORMAL, wxFONTWEIGHT_NORMAL,

false

wxT

(

"Tahoma"

)));

184

itemFlexGridSizer3->Add(

m_StarType

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

186

wxArrayString m_SubmissionTypeStrings;

189 m_SubmissionType

->SetToolTip(

(

"If you select the correct type of submission, this tool will suggest the required and recommended qualifiers needed to help the submission be processed more quickly by GenBank staff."

));

190

itemFlexGridSizer3->Add(

m_SubmissionType

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

192

itemFlexGridSizer3->Add(5, 5, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

194 m_IntroText

new

wxTextCtrl( itemPanel1,

ID_INTRO_TEXT

, wxEmptyString, wxDefaultPosition, wxDefaultSize, wxTE_MULTILINE|wxTE_READONLY|wxTE_RICH|wxTE_AUTO_URL );

195

itemBoxSizer2->Add(

m_IntroText

, 0, wxGROW|wxALL, 5);

253 Vector Contamination:\r\n\ 254 Vector contamination should be removed before submitting your sequences to GenBank.\r\n\ 255 Click the Vector Trim Tool button below if you have not yet screened your sequences for vector.\r\n\ 257 https://www.ncbi.nlm.nih.gov/Sequin/sequin.hlp.html#VectorScreen\r\n\ 262 Welcome to the Sequin Bulk DNA Sequence Submission Wizard!\r\n\ 264 Use this tool if your sequences are from:\r\n\ 265 -uncultured samples\r\n\ 266 -the same gene region (for example: all 16S rRNA or all nifH)\r\n\ 269 -FASTA formatted nucleotide sequence text file or alignment file\r\n\ 270 -Unique clone names\r\n\ 271 -Isolation source (for example, freshwater lake at 100m depth)\r\n\ 272 or hostname (for example, Cocos nucifera) \r\n\ 278 Welcome to the Virus Sequence Submission Wizard!\r\n\ 279 Use this tool if you are submitting:\r\n\ 280 -virus sequences\r\n\ 281 -viroid sequences\r\n\ 284 -FASTA formatted nucleotide sequence text file or alignment file\r\n\ 285 -Unique isolate/strain names\r\n\ 286 -Country, host, collection-date, segment, genotype, and/or serotype may be required for certain viruses and is requested for all virus submissions\r\n\ 288 Feature Annotation:\r\n\ 289 Please use the assistance provided in the wizard to annotate the features your submission or annotate your submissions in the record viewer.\r\n\ 290 If you do not provide feature annotation, assigning of Accession numbers will be delayed.\r\n\ 296 Welcome to the Cultured rRNA-ITS-IGS Submission Wizard!\r\n\ 298 Use this tool for rRNA, ITS, or IGS sequences from:\r\n\ 299 - Cultured, pure strains of Bacteria, Archaea, or Fungi\r\n\ 300 - Vouchered Fungi\r\n\ 301 - Plant, animal or other eukaryotic sequences\r\n\ 303 This tool is NOT for uncultured samples. Use the uncultured sample wizard if you are submitting sequences from an uncultured source.\r\n\ 306 - FASTA formatted nucleotide sequence text file or alignment file\r\n\ 307 - Organism names\r\n\ 308 - Strain names for bacteria, and archaea\r\n\ 309 - Strain or specimen-vouchers for fungi\r\n\ 310 - Specimen vouchers or isolate codes for plants and animals\r\n\ 312 Feature Annotation:\r\n\ 313 Please use the wizard to annotate features in your sequences or annotate your submissions in the record viewer.\r\n\ 314 If you do not provide feature annotation, assigning of Accession numbers will be delayed.\r\n\ 320 Welcome to the TSA Submission Wizard!\r\n\ 321 Use this tool for computationally assembled sequences from primary\r\n\ 322 data such as ESTs, traces and Next Generation Sequencing\r\n\ 323 Technologies. TSA sequence records differ from EST and GenBank\r\n\ 324 records because there are no physical counterparts to the assemblies.\r\n\ 326 Prior to preparing your TSA submission please make sure your\r\n\ 327 assemblies conform to the following standards:\r\n\ 329 -Screen your sequences for vector contamination and remove any\r\n\ 330 vector sequence.\r\n\ 331 -Remove any sequences less than 200bp in length.\r\n\ 332 -Trim any sequences having more than 10% n's or containing greater\r\n\ 333 than 14 n's in a row.\r\n\ 339 Welcome to the Intergenic Spacer Submission Wizard!\r\n\ 341 Use this tool for submitting intergenic spacer sequences.\r\n\ 342 Do not use this tool for submitting complete genomes.\r\n\ 344 Do not use this wizard if you are submitting rRNA-IGS sequences.\r\n\ 345 If you are submitting rRNA-IGS sequences select the rRNA/ITS/IGS wizard instead.\r\n\ 348 - FASTA formatted nucleotide sequence text file or alignment file\r\n\ 349 - Organism names\r\n\ 350 - Unique Source information\r\n\ 356 Welcome to the Microsatellite Wizard!\r\n\ 358 Use this tool for submitting Microsatellite sequences.\r\n\ 361 - FASTA formatted nucleotide sequence text file\r\n\ 362 - Organism names\r\n\ 363 - Unique microsatellite names or clone names\r\n\ 369 Welcome to the D-loop & Control Region Wizard!\r\n\ 371 Use this tool for submitting D-loop or Control Region sequences.\r\n\ 374 - FASTA formatted nucleotide sequence text file\r\n\ 375 - Organism names\r\n\ 376 - Unique source information (such as isolate, haplotype, or specimen- voucher)\r\n\ 383 Welcome to the WGS wizard!\r\n\ 385 Use this tool for submitting Whole Genome Shotgun Submissions to NCBI. \r\n\ 386 This tool is for microbial genomes without annotation. Your file should include sequences from one organism only.\r\n\ 388 Prior to preparing your WGS submission, please make sure your sequences and file conform to the following standards:\r\n\ 389 -WGS contigs should not have any Ns representing gaps. If there are gaps in your sequence, you will need to split the sequences at the gaps. \r\n\ 390 -do not include terminal N's\r\n\ 391 -do not include any sequences shorter than 200 nt \r\n\ 392 -do not include sequences containing more than 10% N's or large regions of low quality sequence\r\n\ 393 -file should not contain more than 10,000 sequences\r\n\ 395 For more information about WGS submissions, please see: \r\n\ 400 Welcome to the Standard Submission Preparation Tool!\r\n\ 402 The Standard Submission preparation tool may be used for any type of nucleotide sequence data except EST (expressed sequence tags), GSS (genome survey sequences), and STS (sequence tagged sites) submissions. Do not use this tool for EST, GSS, or STS submissions.\r\n\ 404 Please review the GenBank data policies before proceeding:\r\n\ 405 https://www.ncbi.nlm.nih.gov/genbank/submit_types \r\n\ 432

star->SetLabel(

wxT

(

"*"

));

434

star->SetLabel(

wxT

(

" "

));

441

wxWindow* w = this->GetParent();

465

objects::CSeqdesc_CI orig_citsub = parent->

GetCitSubPub

();

467 gen

->Assign(orig_citsub->GetPub().GetPub().Get().front()->GetGen());

485 label

"Valid alternate email address is missing"

;

509

objects::CSeqdesc_CI orig_citsub = parent->

GetCitSubPub

();

511 gen

->Assign(orig_citsub->GetPub().GetPub().Get().front()->GetGen());

529 if

(dlg.ShowModal() == wxID_OK) {

542 error

"You must provide a valid alternate email address."

;

545

wxOK | wxICON_ERROR,

this

);

624 switch

(wizard_type) {

687 if

(new_wizard_type != wizard_type) {

701 if

(event.GetMouseEvent().ButtonDown()) {

702

wxTextCtrl* text_ctrl =

dynamic_cast<

wxTextCtrl*

>

(

event

.GetEventObject());

704

wxString

str

= text_ctrl->GetValue();

705

wxString url =

str

.substr(event.GetURLStart(),

event

.GetURLEnd() -

event

.GetURLStart() + 1);

User-defined methods of the data storage class.

@ eWizardType_uncultured_samples

@ eWizardType_microsatellite

@ eWizardType_rrna_its_igs

void OnEditSubmitterInfoClicked(wxHyperlinkEvent &event)

wxEVT_COMMAND_HYPERLINK event handler for ID_HYPERLINKCTRL5

void x_UpdateSubmitBlock(CRef< objects::CSubmit_block > new_block, CRef< objects::CCit_gen > new_gen, string alt_email)

void Init()

Initialises member variables.

void x_SetSubmissionNotReady(string error)

void OnClickSubmitterSummary(wxMouseEvent &event)

wxEVT_LEFT_DOWN event handler for wxID_STATIC

CSubPrep_panel * x_GetParent()

bool Create(wxWindow *parent, wxWindowID id=10090, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

Creation.

wxStaticText * m_StarSubmitter

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void CreateControls()

Creates the controls and sizers.

void x_SetIntroText(CSourceRequirements::EWizardType wizard_type)

wxStaticText * m_StarType

CSubPrepIntroPanel()

Constructors.

~CSubPrepIntroPanel()

Destructor.

void OnIntroTextClickUrl(wxTextUrlEvent &event)

wxEVT_COMMAND_TEXT_URL event handler for ID_INTRO_TEXT

void x_LaunchSubmitEditor()

CSourceRequirements::EWizardType x_GetWizardTypeFromSelection(int sel)

CSourceRequirements::EWizardType GetWizardTypeFromCtrl()

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

wxListBox * m_SubmissionType

void OnSubmissionTypeSelected(wxCommandEvent &event)

wxEVT_COMMAND_LISTBOX_SELECTED event handler for ID_SUBMISSION_TYPE

static bool ShowToolTips()

Should we show tooltips?

wxTextCtrl * m_SubmitterLabel

void RefreshSubmitterInfoStatus()

static string GetWizardTypeName(unsigned int wizard_type)

string GetWizardField(string field_name)

CRef< objects::CSubmit_block > GetSubmitBlock()

void SetSubmissionNotReady(string error)

string GetWizardTypeField()

objects::CSeqdesc_CI GetCitSubPub()

CSourceRequirements::EWizardType SetWizardType(CSourceRequirements::EWizardType wizard_type)

string GetAltEmailAddress()

void UpdateSubmitBlock(CRef< objects::CSubmit_block > new_block, CRef< objects::CCit_gen > new_gen, string alt_email)

static string GetCitGenProblems(CRef< objects::CCit_gen > gen)

string GetAlternateEmailAddress()

CRef< objects::CSubmit_block > GetSubmitBlock()

static string GetBlockProblems(CRef< objects::CSubmit_block > block)

CRef< objects::CCit_gen > GetCitGen()

void SetAlternateEmailAddress(string alt_email)

void SetPageForError(string errors)

void UnselectReleaseDateChoice()

IWorkbench is the central interface in the application framework.

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

static bool PopupURL(const string &url)

launch an application to handle a URL

void Reset(void)

Reset reference object.

#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 const char label[]

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

const string kReleaseDateConfirmed

vector< TWizardName > TWizardNameList

CSourceRequirements::EWizardType GetWizardTypeFromName(string wizard_name)

bool IsValidEmail(string email)

TWizardNameList GetWizardNameList()

static const wxString s_IGSIntroText

static const wxString s_TSAIntroText

static const wxString s_DefaultIntroText

static const wxString s_VirusesIntroText

static const wxString s_WGSIntroText

static const wxString s_MicrosatelliteIntroText

static const wxString s_DLoopIntroText

static const wxString s_rRNA_ITS_IGSIntroText

static const wxString s_UnculturedSamplesIntroText

static const string kSubmitterInfoComplete

static const wxString s_VectorScreenText

static void s_ShowStar(wxStaticText *star, bool show)

#define ID_HYPERLINKCTRL5

#define ID_SUBMISSION_TYPE

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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