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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gassemblyotherpanel_8cpp_source.html below:

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

47 #include <wx/scrolwin.h> 48 #include <wx/stattext.h> 49 #include <wx/textctrl.h> 50 #include <wx/combobox.h> 86

: m_CmdProcessor(cmdproc), m_Seh(seh)

100

SetExtraStyle(wxWS_EX_VALIDATE_RECURSIVELY);

101

wxPanel::Create( parent,

id

, pos,

size

, style );

106

GetSizer()->SetSizeHints(

this

);

148

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

149

itemPanel1->SetSizer(itemBoxSizer2);

151

wxFlexGridSizer* itemFlexGridSizer2 =

new

wxFlexGridSizer(0, 1, 0, 0);

152

itemBoxSizer2->Add(itemFlexGridSizer2, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

154

wxStaticText* itemStaticText6 =

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"Genome coverage"

), wxDefaultPosition, wxDefaultSize, 0 );

155

itemFlexGridSizer2->Add(itemStaticText6, 0, wxALIGN_LEFT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

159 m_GenomeCoverage

->SetToolTip(

(

"The estimated base coverage across the genome, eg 12x. This can be calculated by dividing the number of bases sequenced by the expected genome size and multiplying that by the percentage of bases that were placed in the final assembly. More simply it is the number of bases sequenced divided by the expected genome size."

));

160

itemFlexGridSizer2->Add(

m_GenomeCoverage

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

162

itemFlexGridSizer2->Add(5, 5, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

164

wxStaticText* itemStaticText1 =

new

wxStaticText( itemPanel1, wxID_STATIC,

(

"Sequencing technology"

), wxDefaultPosition, wxDefaultSize, 0 );

165

itemFlexGridSizer2->Add(itemStaticText1, 0, wxALIGN_LEFT|wxALIGN_CENTER_VERTICAL|wxALL, 5);

168

itemFlexGridSizer2->Add(

m_ScrolledWindow

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

170 m_Sizer

new

wxFlexGridSizer(0, 2, 0, 0);

173 for

(

size_t

index = 0; index <

m_Rows

; ++index) {

176

wxHyperlinkCtrl* itemHyperlinkCtrl2 =

new

wxHyperlinkCtrl( itemPanel1,

ID_SEQTECHHYPERLINK

(

"Add another sequencing technology"

), wxEmptyString, wxDefaultPosition, wxDefaultSize, wxHL_DEFAULT_STYLE );

177

itemFlexGridSizer2->Add(itemHyperlinkCtrl2, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

184

wxArrayString m_SeqTechnologyStrings;

185

m_SeqTechnologyStrings.Add(

(

"ABI3730"

));

186

m_SeqTechnologyStrings.Add(

(

"Sanger"

));

187

m_SeqTechnologyStrings.Add(

(

"454"

));

188

m_SeqTechnologyStrings.Add(

(

"Illumina"

));

189

m_SeqTechnologyStrings.Add(

(

"Illumina GAII"

));

190

m_SeqTechnologyStrings.Add(

(

"Illumina GAIIx"

));

191

m_SeqTechnologyStrings.Add(

(

"Illumina HiSeq"

));

192

m_SeqTechnologyStrings.Add(

(

"Illumina iSeq"

));

193

m_SeqTechnologyStrings.Add(

(

"Illumina MiniSeq"

));

194

m_SeqTechnologyStrings.Add(

(

"Illumina MiSeq"

));

195

m_SeqTechnologyStrings.Add(

(

"Illumina NextSeq"

));

196

m_SeqTechnologyStrings.Add(

(

"Illumina NovaSeq"

));

197

m_SeqTechnologyStrings.Add(

(

"IonTorrent"

));

198

m_SeqTechnologyStrings.Add(

(

"Oxford Nanopore"

));

199

m_SeqTechnologyStrings.Add(

(

"Oxford Nanopore GridION"

));

200

m_SeqTechnologyStrings.Add(

(

"Oxford Nanopore MiniION"

));

201

m_SeqTechnologyStrings.Add(

(

"Oxford Nanopore PromethION"

));

202

m_SeqTechnologyStrings.Add(

(

"PacBio"

));

203

m_SeqTechnologyStrings.Add(

(

"PacBio RS"

));

204

m_SeqTechnologyStrings.Add(

(

"PacBio RSII"

));

205

m_SeqTechnologyStrings.Add(

(

"PacBio Sequel"

));

206

m_SeqTechnologyStrings.Add(

(

"Helicos"

));

207

m_SeqTechnologyStrings.Add(

(

"SOLiD"

));

208

m_SeqTechnologyStrings.Add(

(

"Complete Genomics"

));

210 #ifdef __WXOSX_COCOA__ 211 row

->SetSelection(-1);

214 row

->SetToolTip(

(

"The sequencing machine(s) used to generate the data, eg Illumina MiSeq or 454. Select the sequencing technology from the pulldown list, or type the name of the technology directly in the box."

));

225 m_Sizer

->Add(

row

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

227

itemHyperLink->SetVisitedColour(itemHyperLink->GetNormalColour());

228 m_Sizer

->Add(itemHyperLink, 0, wxALIGN_CENTER_VERTICAL | wxLEFT | wxRIGHT, 0);

235 int

row_width, row_height;

236 row

->GetClientSize(&row_width, &row_height);

238 int

link_width, link_height;

239

itemHyperLink->GetClientSize(&link_width, &link_height);

240 if

(link_height > row_height) {

241

row_height = link_height;

243

row_width += link_width;

313

wxWindow *win =

dynamic_cast<

wxWindow*

>

(

event

.GetEventObject());

318 for

(wxWindowList::iterator child = children.begin(); child != children.end(); ++child)

322

wxSizer *sizer = win->GetContainingSizer();

346

wxComboBox*

row

dynamic_cast<

wxComboBox *

>

(it);

348 row

->SetValue(

wxT

(

""

));

360 for

(

auto

it :

m_User

->GetData()) {

361 if

(it->IsSetLabel() && it->GetLabel().IsStr() &&

362

it->IsSetData() && it->GetData().IsStr()) {

363 const string

label

= it->GetLabel().GetStr();

368

vector<string> techs;

372

wxComboBox*

row

dynamic_cast<

wxComboBox *

>

(rit);

377 while

(techs.size() > num_rows) {

381 auto

s = techs.begin();

383

wxComboBox*

row

dynamic_cast<

wxComboBox *

>

(rit);

387 if

(s == techs.end()) {

413

wxComboBox*

row

dynamic_cast<

wxComboBox *

>

(it);

415 string

new_val =

row

->GetValue().ToStdString();

416 if

(!new_val.empty()) {

424

tech = tech.substr(0, tech.length() - 1);

430

seqtech.SetData().SetStr(tech);

436 const

objects::CComment_rule& rule = rules->FindCommentRule(

"Genome-Assembly-Data"

);

437

rule.ReorderFields(*

m_User

);

456 bool

any_changes =

false

;

458 for

(objects::CBioseq_CI bi(

m_Seh

, objects::CSeq_inst::eMol_na); bi; ++bi)

461 for

(objects::CSeqdesc_CI di(*bi, objects::CSeqdesc::e_User); di; ++di)

463 if

(di && di->IsUser() && di->GetUser().GetObjectType() == objects::CUser_object::eObjectType_StructuredComment &&

464 NStr::Equal

(objects::CComment_rule::GetStructuredCommentPrefix(di->GetUser()),

"Genome-Assembly-Data"

))

470 if

(!di->Equals(*cpy))

473 cmd

->AddCommand(*chg);

484

new_desc->SetUser(*

m_User

);

485

objects::CBioseq_set_Handle parent = bi->GetParentBioseq_set();

486 auto

entry = bi->GetParentEntry();

487 if

(parent && parent.IsSetClass() && parent.GetClass() == objects::CBioseq_set::eClass_nuc_prot)

488

entry = parent.GetParentEntry();

490 cmd

->AddCommand(*cmdAddDesc);

void CreateControls()

Creates the controls and sizers.

void ApplyUser(objects::CUser_object &user)

~CGAssemblyOtherPanel()

Destructor.

void OnAddNewSeqtechnology(wxHyperlinkEvent &event)

wxEVT_COMMAND_HYPERLINK event handler for ID_SEQTECHHYPERLINK

CGAssemblyOtherPanel()

Constructors.

void x_AddRowToWindow(wxWindow *row)

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

Creation.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void OnDeleteSeqtechnology(wxHyperlinkEvent &event)

virtual bool TransferDataFromWindow()

virtual bool TransferDataToWindow()

ICommandProccessor * m_CmdProcessor

objects::CSeq_entry_Handle m_Seh

wxTextCtrl * m_GenomeCoverage

wxScrolledWindow * m_ScrolledWindow

wxFlexGridSizer * m_Sizer

CRef< objects::CUser_object > m_User

virtual void ApplyCommand()

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void Init()

Initialises member variables.

static bool ShowToolTips()

Should we show tooltips?

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

const string kGenomeCoverage

const string kSequencingTechnology

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 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[]

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

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

#define row(bind, expected)

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gassembly__other__panel_8cpp_source.html below:

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gassemblyotherpanel_8cpp_source.html below: