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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/splign__panel_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/packages/pkg_alignment/splign_panel.cpp Source File

48 #include <wx/statbox.h> 49 #include <wx/stattext.h> 50 #include <wx/choice.h> 51 #include <wx/checkbox.h> 52 #include <wx/radiobox.h> 53 #include <wx/msgdlg.h> 77

CSeq_loc::GetTypeInfo()->GetName(), relations);

79 if

(relations.empty()) {

80

errMessage =

wxT

(

"Object cannot be converted to CSeq_loc."

);

87 if

(related.empty()) {

88

errMessage =

wxT

(

"Object cannot be converted to CSeq_loc."

);

97 if

(m_MolType == kProtein && handle.

IsAa

()) {

99

}

else if

(m_MolType == kNucleotide && handle.

IsNa

()) {

105 if

(desc_iter) molInfo = &desc_iter->

GetMolinfo

();

110 if

(m_MolType == kGenomic)

118 if

(m_MolType == kCDNA)

126

errMessage = e.

GetMsg

();

128 catch

(

const

exception& e) {

129

errMessage = e.

what

();

132 if

(errMessage.empty()) {

135

errMessage =

wxT

(

"Object is not a Genomic sequence."

);

138

errMessage =

wxT

(

"Object is not a cDNA/Transcript sequence."

);

141

errMessage =

wxT

(

"Object is not a protein sequence."

);

144

errMessage =

wxT

(

"Object is not a nucleotide sequence."

);

164 Create

(parent,

id

, pos,

size

, style, visible);

169

SetExtraStyle(wxWS_EX_VALIDATE_RECURSIVELY);

171

CAlgoToolManagerParamsPanel::Create( parent,

id

, pos,

size

, style );

180

GetSizer()->SetSizeHints(

this

);

204 CSplignPanel

* itemCAlgoToolManagerParamsPanel1 =

this

;

206

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

207

itemCAlgoToolManagerParamsPanel1->SetSizer(itemBoxSizer2);

210

itemBoxSizer2->Add(

m_GenomicList

, 1, wxGROW|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(1, -1)).x);

213

itemBoxSizer2->Add(

m_cDNAList

, 1, wxGROW|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(1, -1)).x);

215

wxBoxSizer* itemBoxSizer5 =

new

wxBoxSizer(wxHORIZONTAL);

216

itemBoxSizer2->Add(itemBoxSizer5, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

218

wxStaticText* itemStaticText6 =

new

wxStaticText( itemCAlgoToolManagerParamsPanel1, wxID_STATIC,

(

"cDNA strand"

), wxDefaultPosition, wxDefaultSize, 0 );

219

itemBoxSizer5->Add(itemStaticText6, 0, wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(5, -1)).x);

221

wxArrayString itemChoice7Strings;

222

itemChoice7Strings.Add(

(

"plus"

));

223

itemChoice7Strings.Add(

(

"minus"

));

224

itemChoice7Strings.Add(

(

"both"

));

225

wxChoice* itemChoice7 =

new

wxChoice( itemCAlgoToolManagerParamsPanel1,

ID_CHOICE3

, wxDefaultPosition, wxDefaultSize, itemChoice7Strings, 0 );

226

itemBoxSizer5->Add(itemChoice7, 0, wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(5, -1)).x);

228

wxArrayString itemChoice8Strings;

229

itemChoice8Strings.Add(

(

"EST"

));

230

itemChoice8Strings.Add(

(

"mRNA"

));

231

wxChoice* itemChoice8 =

new

wxChoice( itemCAlgoToolManagerParamsPanel1,

ID_CHOICE4

, wxDefaultPosition, wxDefaultSize, itemChoice8Strings, 0 );

232

itemBoxSizer5->Add(itemChoice8, 0, wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(5, -1)).x);

234

wxCheckBox* itemCheckBox9 =

new

wxCheckBox( itemCAlgoToolManagerParamsPanel1,

ID_CHECKBOX3

(

"EndGap Detection"

), wxDefaultPosition, wxDefaultSize, 0 );

235

itemCheckBox9->SetValue(

false

);

236

itemBoxSizer5->Add(itemCheckBox9, 0, wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(5, -1)).x);

238

wxCheckBox* itemCheckBox10 =

new

wxCheckBox( itemCAlgoToolManagerParamsPanel1,

ID_CHECKBOX4

(

"PolyA Detection"

), wxDefaultPosition, wxDefaultSize, 0 );

239

itemCheckBox10->SetValue(

false

);

240

itemBoxSizer5->Add(itemCheckBox10, 0, wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(5, -1)).x);

242

wxFlexGridSizer* itemFlexGridSizer11 =

new

wxFlexGridSizer(0, 4, 0, 0);

243

itemBoxSizer2->Add(itemFlexGridSizer11, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

245

wxStaticText* itemStaticText12 =

new

wxStaticText( itemCAlgoToolManagerParamsPanel1, wxID_STATIC,

(

"Min compartment identity"

), wxDefaultPosition, wxDefaultSize, 0 );

246

itemFlexGridSizer11->Add(itemStaticText12, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(2, -1)).x);

248

wxTextCtrl* itemTextCtrl13 =

new

wxTextCtrl( itemCAlgoToolManagerParamsPanel1,

ID_TEXTCTRL7

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

249

itemFlexGridSizer11->Add(itemTextCtrl13, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(2, -1)).x);

251

wxStaticText* itemStaticText14 =

new

wxStaticText( itemCAlgoToolManagerParamsPanel1, wxID_STATIC,

(

"Maximum Genomic Extent"

), wxDefaultPosition, wxDefaultSize, 0 );

252

itemFlexGridSizer11->Add(itemStaticText14, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(2, -1)).x);

254

wxTextCtrl* itemTextCtrl15 =

new

wxTextCtrl( itemCAlgoToolManagerParamsPanel1,

ID_TEXTCTRL6

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

255

itemFlexGridSizer11->Add(itemTextCtrl15, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(2, -1)).x);

257

wxStaticText* itemStaticText16 =

new

wxStaticText( itemCAlgoToolManagerParamsPanel1, wxID_STATIC,

(

"Min exon identity"

), wxDefaultPosition, wxDefaultSize, 0 );

258

itemFlexGridSizer11->Add(itemStaticText16, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(2, -1)).x);

260

wxTextCtrl* itemTextCtrl17 =

new

wxTextCtrl( itemCAlgoToolManagerParamsPanel1,

ID_TEXTCTRL8

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

261

itemFlexGridSizer11->Add(itemTextCtrl17, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(2, -1)).x);

263

wxStaticText* itemStaticText18 =

new

wxStaticText( itemCAlgoToolManagerParamsPanel1, wxID_STATIC,

(

"Compartment penalty"

), wxDefaultPosition, wxDefaultSize, 0 );

264

itemFlexGridSizer11->Add(itemStaticText18, 0, wxALIGN_RIGHT|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(2, -1)).x);

266

wxTextCtrl* itemTextCtrl19 =

new

wxTextCtrl( itemCAlgoToolManagerParamsPanel1,

ID_TEXTCTRL9

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

267

itemFlexGridSizer11->Add(itemTextCtrl19, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(2, -1)).x);

269

wxStaticText* itemStaticText20 =

new

wxStaticText( itemCAlgoToolManagerParamsPanel1, wxID_STATIC,

(

"Maximum intron length"

), wxDefaultPosition, wxDefaultSize, 0 );

270

itemFlexGridSizer11->Add(itemStaticText20, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(5, -1)).x);

272

wxTextCtrl* itemTextCtrl21 =

new

wxTextCtrl( itemCAlgoToolManagerParamsPanel1,

ID_TEXTCTRL13

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

273

itemFlexGridSizer11->Add(itemTextCtrl21, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, wxDLG_UNIT(itemCAlgoToolManagerParamsPanel1, wxSize(5, -1)).x);

276

itemChoice7->SetValidator( wxGenericValidator(&

GetData

().m_cDNA_strand) );

277

itemChoice8->SetValidator( wxGenericValidator(&

GetData

().m_DiscType) );

278

itemCheckBox9->SetValidator( wxGenericValidator(&

GetData

().m_EndGapDetect) );

279

itemCheckBox10->SetValidator( wxGenericValidator(&

GetData

().m_PolyADetect) );

325 if

(!CAlgoToolManagerParamsPanel::TransferDataFromWindow())

360

TransferDataToWindow();

vector< TRelation > TRelationVector

static void FindRelations(objects::CScope &scope, const CObject &obj, const string &to_type_in, TRelationVector &relations)

vector< SObject > TObjects

@ fConvert_NoExpensive

do not perform any expensive tests (such as fetching from the network)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

CObjectListWidgetSel * m_GenomicList

bool Create(wxWindow *parent, wxWindowID id=ID_CSPLIGNPANEL, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCLIP_CHILDREN|wxTAB_TRAVERSAL, bool visibale=true)

virtual void LoadSettings()

wxBitmap GetBitmapResource(const wxString &name)

void RestoreDefaults()

override in derived classes

CSplignParams & GetData()

virtual void SaveSettings() const

override in derived classes

wxIcon GetIconResource(const wxString &name)

static bool ShowToolTips()

TConstScopedObjects m_cDNASeqs

SConstScopedObject m_GenomicSeq

virtual void SetRegistryPath(const string &path)

CAlgoToolManagerParamsPanel.

CMolTypeValidator m_GenomicListAccValidator

CMolTypeValidator m_CDNAListAccValidator

CObjectListWidgetSel * m_cDNAList

void SetObjects(map< string, TConstScopedObjects > *genomic, map< string, TConstScopedObjects > *na)

virtual bool TransferDataFromWindow()

vector< SConstScopedObject > TConstScopedObjects

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TBiomol GetBiomol(void) const

Get the Biomol member data.

const TMolinfo & GetMolinfo(void) const

Get the variant data.

@ e_Molinfo

info on the molecule and techniques

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

USING_SCOPE(ncbi::objects)

static const char * kGenomicList

static const char * kCDNAList

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