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

46 #include <wx/stattext.h> 86

: m_TopSeqEntry(seh), m_DefaultKey(

key

CBulkCmdPanel

(add_location_panel)

100

CBulkCmdPanel::Create( parent,

id

, pos,

size

, style );

105

GetSizer()->SetSizeHints(

this

);

140 m_QualFeat

->SetData().SetImp().SetKey(

"misc_feature"

);

153

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

154

itemCBulkCmdPanel1->SetSizer(itemBoxSizer2);

156

wxBoxSizer* itemBoxSizer3 =

new

wxBoxSizer(wxHORIZONTAL);

157

itemBoxSizer2->Add(itemBoxSizer3, 0, wxALIGN_LEFT|wxALL, 5);

159

wxBoxSizer* itemBoxSizer4 =

new

wxBoxSizer(wxVERTICAL);

160

itemBoxSizer3->Add(itemBoxSizer4, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

162

wxStaticText* itemStaticText5 =

new

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

"Feature Type"

), wxDefaultPosition, wxDefaultSize, 0 );

163

itemBoxSizer4->Add(itemStaticText5, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

165

wxArrayString m_FeatureTypeStrings;

167

itemBoxSizer4->Add(

m_FeatureType

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

172

wxFlexGridSizer* itemFlexGridSizer8 =

new

wxFlexGridSizer(0, 2, 0, 0);

173

itemBoxSizer2->Add(itemFlexGridSizer8, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

175

wxStaticText* itemStaticText9 =

new

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

"Gene Symbol"

), wxDefaultPosition, wxDefaultSize, 0 );

176

itemFlexGridSizer8->Add(itemStaticText9, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

178 m_Locus

new

wxTextCtrl( itemCBulkCmdPanel1,

ID_TEXTCTRL11

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

179

itemFlexGridSizer8->Add(

m_Locus

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

181

wxStaticText* itemStaticText11 =

new

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

"Gene Description"

), wxDefaultPosition, wxDefaultSize, 0 );

182

itemFlexGridSizer8->Add(itemStaticText11, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

184 m_GeneDesc

new

wxTextCtrl( itemCBulkCmdPanel1,

ID_TEXTCTRL12

, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

185

itemFlexGridSizer8->Add(

m_GeneDesc

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

187

wxStaticText* itemStaticText13 =

new

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

"Comment"

), wxDefaultPosition, wxDefaultSize, 0 );

188

itemFlexGridSizer8->Add(itemStaticText13, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

190 m_Comment

new

wxTextCtrl( itemCBulkCmdPanel1,

ID_TEXTCTRL14

, wxEmptyString, wxDefaultPosition, wxSize(300, 70), wxTE_MULTILINE );

191

itemFlexGridSizer8->Add(

m_Comment

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

196

itemBoxSizer2->Add(

m_Location

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

199

itemBoxSizer2->Add(500, 0, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 0);

229

vector<string> listed_feat;

233

listed_feat.push_back(

"Gene"

);

234

listed_feat.push_back(

"misc_feature"

);

235

existing.

insert

(listed_feat[0]);

236

existing.

insert

(listed_feat[1]);

239 ITERATE

(vector<const CFeatListItem *>, feat_it, featlist) {

242 int

feat_type = item.

GetType

();

247 types

[pair<int,int>(feat_type,feat_subtype)] = desc;

248 if

(existing.

find

(desc) == existing.

end

()) {

250

listed_feat.push_back(desc);

256 for

(

size_t i

= 0;

< listed_feat.size(); ++

) {

260 if

(find(listed_feat.begin(), listed_feat.end(),

m_DefaultKey

) != listed_feat.end()) {

312

objects::CBioseq_CI b_iter(

m_TopSeqEntry

, objects::CSeq_inst::eMol_na);

313 for

( ; b_iter ; ++b_iter ) {

340

feat->SetData().SetImp().SetKey(

key

);

342

feat->SetComment(comment);

344

feat->SetLocation().Assign(*loc);

347

feat->SetPartial(

true

);

355

new_gene->SetData().SetGene().SetLocus(gene_symbol);

357

new_gene->SetData().SetGene().SetDesc(gene_desc);

360

new_gene->SetComment(comment);

362

new_gene->SetLocation().Assign(*loc);

365

new_gene->SetPartial(

true

);

376 return "You must select feature type!"

;

378

objects::CBioseq_CI b_iter(

m_TopSeqEntry

, objects::CSeq_inst::eMol_na);

379 for

( ; b_iter ; ++b_iter ) {

380

objects::CSeq_entry_Handle seh = b_iter->GetSeq_entry_Handle();

383 return "You must specify valid location values!"

;

386 return "Unknown error"

;

432

feat.SetQual().push_back(q);

435

&& feat.GetData().GetImp().IsSetKey() && feat.GetData().GetImp().GetKey() ==

"repeat_region"

)

437

feat.SetData().SetImp().SetKey(

"mobile_element"

);

449 string val

= (*it)->GetVal();

450 string

qual = (*it)->GetQual();

451 if

(qual ==

"locus"

)

452

gene.SetData().SetGene().SetLocus(

val

);

453 if

(qual ==

"locus_tag"

)

454

gene.SetData().SetGene().SetLocus_tag(

val

);

455 if

(qual ==

"allele"

)

456

gene.SetData().SetGene().SetAllele(

val

);

458

gene.SetData().SetGene().SetMaploc(

val

);

459 if

(qual ==

"gene_synonym"

)

460

gene.SetData().SetGene().SetSyn().push_back(

val

);

@ eExtreme_Biological

5' and 3'

static bool s_IsRNAFeature(int feat_subtype)

USING_SCOPE(ncbi::objects)

#define ID_FEATURE_TYPE_LISTBOX

CBulkLocationPanel * m_Location

bool m_add_location_panel

virtual bool ShouldAddToExisting()

virtual CRef< objects::CSeq_loc > GetLocForBioseq(const objects::CBioseq &bioseq)

virtual CRef< CCmdComposite > GetCommand()

void CreateControls()

Creates the controls and sizers.

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

Creation.

~CBulkOtherAddPanel()

Destructor.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void OnFeatureTypeListboxSelected(wxCommandEvent &event)

wxEVT_COMMAND_LISTBOX_SELECTED event handler for ID_FEATURE_TYPE_LISTBOX

void AddOneCommand(const objects::CBioseq_Handle &bsh, CRef< CCmdComposite > cmd) override

CBulkOtherAddPanel()

Constructors.

void Init()

Initialises member variables.

CRef< objects::CSeq_feat > m_QualFeat

CGBQualPanel * m_GBQualPanel

void x_AddGeneQuals(objects::CSeq_feat &gene)

wxBoxSizer * m_GBQualSizer

virtual string GetErrorMessage()

wxListBox * m_FeatureType

void x_ChangeFeatureType(const string &key)

static bool ShowToolTips()

Should we show tooltips?

objects::CSeq_entry_Handle m_TopSeqEntry

void x_AddQuals(objects::CSeq_feat &feat)

CFeatListItem - basic configuration data for one "feature" type.

string GetDescription() const

static bool s_IsRarelyUsedOrDiscouragedFeatureType(int subtype)

virtual bool TransferDataToWindow()

virtual bool TransferDataFromWindow()

void PopulateGBQuals(objects::CSeq_feat &seq_feat)

@Gb_qual.hpp User-defined methods of the data storage class.

static bool IsRegulatory(ESubtype subtype)

namespace ncbi::objects::

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

static const struct type types[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

vector< const objects::CFeatListItem * > GetSortedFeatList(objects::CSeq_entry_Handle seh, size_t max=numeric_limits< size_t >::max())

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

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

Case-insensitive equality of a substring with another string.

vector< CRef< CGb_qual > > TQual

const TQual & GetQual(void) const

Get the Qual member data.

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

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

const struct ncbi::grid::netcache::search::fields::KEY key

bool AlreadyHasFeature(objects::CBioseq_Handle bh, string key, string comment)

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/bulk__other__add__panel_8cpp_source.html below:

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bulkotheradd__panel_8cpp_source.html below: