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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqtechdlg_8cpp_source.html below:

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

45 #include <wx/button.h> 53 static const string kRaw

"Raw"

;

89

wxWindowID

id

const

wxString& caption,

const

wxPoint& pos,

const

wxSize&

size

long

style )

90

: m_TopSeqEntry(seh), m_WizardType(wizard_type)

96 Create

(parent,

id

, caption, pos,

size

, style);

104 bool CSeqTechDlg::Create

( wxWindow* parent, wxWindowID

id

const

wxString& caption,

const

wxPoint& pos,

const

wxSize&

size

long

style )

107

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

108

wxFrame::Create( parent,

id

, caption, pos,

size

, style );

113

GetSizer()->SetSizeHints(

this

);

157

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

158

itemDialog1->SetSizer(itemBoxSizer2);

161

itemBoxSizer2->Add(

m_PanelSizer

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

163

wxStaticBox* itemStaticBoxSizer4Static =

new

wxStaticBox(itemDialog1,

wxID_ANY

(

"These sequence(s) are"

));

164

wxStaticBoxSizer* itemStaticBoxSizer4 =

new

wxStaticBoxSizer(itemStaticBoxSizer4Static, wxHORIZONTAL);

165

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

167 m_RawBtn

new

wxRadioButton( itemDialog1,

ID_RAW_BTN

(

"raw sequence reads (not assembled)"

), wxDefaultPosition, wxDefaultSize, 0 );

169

itemStaticBoxSizer4->Add(

m_RawBtn

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

173

itemStaticBoxSizer4->Add(

m_AssembledBtn

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

175

wxBoxSizer* itemBoxSizer7 =

new

wxBoxSizer(wxHORIZONTAL);

176

itemBoxSizer2->Add(itemBoxSizer7, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

178

wxButton* itemButton8 =

new

wxButton( itemDialog1, wxID_OK,

(

"Accept"

), wxDefaultPosition, wxDefaultSize, 0 );

179

itemBoxSizer7->Add(itemButton8, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

181

wxButton* itemButton9 =

new

wxButton( itemDialog1, wxID_CANCEL,

(

"Cancel"

), wxDefaultPosition, wxDefaultSize, 0 );

182

itemBoxSizer7->Add(itemButton9, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

241

vector<string> values;

244 ITERATE

(vector<string>, it, values) {

262 "Overlapping sequence"

263 "Overlapping sequences"

};

270 return "BLAST is not an assembly program. Please provide valid assembly program information."

;

272 string

program = assem;

274 if

(pos != string::npos) {

275

program = assem.substr(0, pos);

279 return "The assembly program name is not valid. Please enter the name of the program used to assemble these sequences."

;

282 if

(pos == string::npos) {

283 return "You must provide the version as well as the name of the assembly program."

;

297 "Overlapping sequence"

298 "Overlapping sequences" 319 const

objects::CUser_field& field = user->GetField(field_name);

320 if

(field.IsSetData() && field.GetData().IsStr()) {

321 val

= field.GetData().GetStr();

323

}

catch

(

const

exception&) {

333 return "Missing Sequencing Technology!"

;

339 return "You must select whether the sequences are assembled or raw."

;

342 return "Do not use TSA wizard for unassembled Sanger or ABI sequences"

;

344 return "Raw sequence reads generated by next generation sequencing technologies should be submitted to the Sequence Read Archive (SRA), not GenBank. Please see: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi"

;

353 return "Please provide the assembly program and version in the form."

;

355 return "BLAST is not an assembly program. Please provide valid assembly program information."

;

363 return "Sequencing technology is not a valid answer. Please enter the specific type of technology used to obtain these sequences."

;

367 return "'"

+ seq_tech +

"' is not a sequencing technology. Please only enter the type of technology that was used to generate your sequences."

;

376 string

raw_or_assembled =

""

;

378

raw_or_assembled =

kRaw

;

382 return

raw_or_assembled;

401

objects::CBioseq_CI b_iter(

m_TopSeqEntry

, objects::CSeq_inst::eMol_na);

402 for

( ; b_iter ; ++b_iter ) {

406

new_desc->SetUser(*new_user);

409 for

(objects::CSeqdesc_CI desc_ci( *b_iter, objects::CSeqdesc::e_User);

412 const

objects::CUser_object& u = desc_ci->GetUser();

413 if

(u.IsSetType() && u.GetType().IsStr() &&

NStr::EqualNocase

(u.GetType().GetStr(),

"StructuredComment"

)) {

415 const

objects::CUser_field& prefix = desc_ci->GetUser().GetField(

"StructuredCommentPrefix"

);

416 if

(prefix.IsSetData() && prefix.GetData().IsStr()

420 cmd

->AddCommand (*ecmd);

423

}

catch

(

const

exception&) {

428

objects::CBioseq_set_Handle bssh = b_iter->GetParentBioseq_set();

429 if

(bssh && bssh.IsSetClass() && bssh.GetClass() == objects::CBioseq_set::eClass_nuc_prot) {

450

problem =

"Unknown error"

;

458

objects::CBioseq_CI b_iter(

m_TopSeqEntry

, objects::CSeq_inst::eMol_na);

459 for

( ; b_iter ; ++b_iter ) {

460

objects::CSeqdesc_CI it (*b_iter, objects::CSeqdesc::e_User);

462 if

(it->GetUser().IsSetType()

463

&& it->GetUser().GetType().IsStr()

465 ITERATE

(objects::CUser_object::TData, field_it, it->GetUser().GetData()) {

466 if

((*field_it)->IsSetLabel()

467

&& (*field_it)->GetLabel().IsStr()

468

NStr::EqualNocase

((*field_it)->GetLabel().GetStr(),

"StructuredCommentPrefix"

)

469

&& (*field_it)->IsSetData()

470

&& (*field_it)->GetData().IsStr()

471

NStr::EqualNocase

((*field_it)->GetData().GetStr(),

"##Assembly-Data-START##"

)) {

481 m_EditedObj

->SetType().SetStr(

"StructuredComment"

);

482

objects::CUser_field& prefix =

m_EditedObj

->SetField(

"StructuredCommentPrefix"

);

483

prefix.SetData().SetStr(

"##Assembly-Data-START##"

);

484

objects::CUser_field& suffix =

m_EditedObj

->SetField(

"StructuredCommentSuffix"

);

485

suffix.SetData().SetStr(

"##Assembly-Data-END##"

);

virtual CRef< CCmdComposite > GetCommand()

CSeqTechDlg()

Constructors.

CSourceRequirements::EWizardType m_WizardType

static string CheckSequencingTechnology(CRef< objects::CUser_object > user, CSourceRequirements::EWizardType wizard_type, string raw_or_assembled)

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

CRef< objects::CUser_object > m_EditedObj

string x_GetRawOrAssembled()

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

bool Create(wxWindow *parent, wxWindowID id=10014, const wxString &caption=_("Sequencing Technology"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

objects::CSeq_entry_Handle m_TopSeqEntry

wxBoxSizer * m_PanelSizer

~CSeqTechDlg()

Destructor.

CSequencingTechnologyPanel * m_Panel

wxRadioButton * m_AssembledBtn

virtual string GetErrorMessage()

void CreateControls()

Creates the controls and sizers.

static bool x_IsSpecialTech(string tech)

void Init()

Initialises member variables.

void x_GetSeqTechUserFromSeqEntry()

void OnAssembledBtnSelected(wxCommandEvent &event)

wxEVT_COMMAND_RADIOBUTTON_SELECTED event handler for ID_ASSEMBLED_BTN

static bool ShowToolTips()

Should we show tooltips?

void OnRawBtnSelected(wxCommandEvent &event)

wxEVT_COMMAND_RADIOBUTTON_SELECTED event handler for ID_RAW_BTN

virtual bool TransferDataFromWindow()

CRef< objects::CUser_object > GetUser_object() const

virtual bool TransferDataToWindow()

static string GetWizardFieldFromSeqEntry(objects::CSeq_entry_Handle entry, string field_name)

static CRef< CCmdComposite > SetWizardFieldInSeqEntry(objects::CSeq_entry_Handle entry, string field_name, string value)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#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 SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

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

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

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

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

Case-insensitive equality of a substring with another string.

@ eNocase

Case insensitive compare.

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

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

static const string kAssembled

bool s_IsBadMethod(string method)

static const int k_NumBadAssemblyPrograms

string s_IsAssemblyMethodValid(string assem)

static string s_GetFieldValFromUserObj(CRef< objects::CUser_object > user, string field_name)

static const int k_NumBadMethods

static string s_BadMethods[]

static const string kRawOrAssembled

static string s_BadAssemblyPrograms[]

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