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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/add__linkage__to__gaps_8cpp_source.html below:

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

33 #include "wx/wxprec.h" 98

wxWindowID

id

,

const

wxString& caption,

const

wxPoint& pos,

const

wxSize&

size

,

long

style )

101  Create

(parent,

id

, caption, pos,

size

, style);

110

wxWindowID

id

,

const

wxString& caption,

const

wxPoint& pos,

const

wxSize&

size

,

long

style )

113 

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

114

wxDialog::Create( parent,

id

, caption, pos,

size

, style );

119

GetSizer()->SetSizeHints(

this

);

160

wxBoxSizer* itemBoxSizer2 =

new

wxBoxSizer(wxVERTICAL);

161

itemDialog1->SetSizer(itemBoxSizer2);

163

wxFlexGridSizer* itemFlexGridSizer3 =

new

wxFlexGridSizer(0, 2, 0, 0);

164

itemBoxSizer2->Add(itemFlexGridSizer3, 0, wxALIGN_CENTER_HORIZONTAL | wxALL, 2);

170

wxArrayString type_str, linkage_str, linkage_evidence_str;

171

type_str.Add(

"within"

);

172

type_str.Add(

"between"

);

173

type_str.Add(

"short-arm"

);

174

type_str.Add(

"heterochromatin"

);

175

type_str.Add(

"telomere"

);

176

type_str.Add(

"centromere"

);

177

type_str.Add(

"repeat"

);

178

type_str.Add(

"contamination"

);

179

type_str.Add(

"unknown"

);

180

type_str.Add(

"other"

);

187

linkage_str.Add(

_

(

"Within Scaffolds"

));

188

linkage_str.Add(

_

(

"Between Scaffolds"

));

190  for

(CEnumeratedTypeValues::TValues::const_iterator

i

= linkage_evidence_values.begin();

i

!= linkage_evidence_values.end(); ++

i

)

192

linkage_evidence_str.Add(wxString(

i

->first));

195

wxStaticText* itemStaticText10 =

new

wxStaticText( itemDialog1, wxID_STATIC,

_

(

"Gap Type"

), wxDefaultPosition, wxDefaultSize, 0 );

196

itemFlexGridSizer3->Add(itemStaticText10, 1, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL |wxALL, 5);

200

itemFlexGridSizer3->Add(

m_GapType

, 1, wxALIGN_LEFT | wxGROW | wxALIGN_CENTER_VERTICAL |wxALL, 5);

203

wxStaticText* itemStaticText11 =

new

wxStaticText( itemDialog1, wxID_STATIC,

_

(

"Linkage"

), wxDefaultPosition, wxDefaultSize, 0 );

204

itemFlexGridSizer3->Add(itemStaticText11, 1, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL |wxALL, 5);

208

itemFlexGridSizer3->Add(

m_Linkage

, 1, wxALIGN_LEFT | wxGROW | wxALIGN_CENTER_VERTICAL |wxALL, 5);

211

wxStaticText* itemStaticText12 =

new

wxStaticText( itemDialog1, wxID_STATIC,

_

(

"Linkage Evidence"

), wxDefaultPosition, wxDefaultSize, 0 );

212

itemFlexGridSizer3->Add(itemStaticText12, 1, wxALIGN_RIGHT | wxALIGN_CENTER_VERTICAL |wxALL, 5);

214  m_LinkageEvidence

=

new

wxChoice(itemDialog1,

wxID_ANY

, wxDefaultPosition, wxDefaultSize, linkage_evidence_str,0,wxDefaultValidator,

"Linkage Evidence"

);

216

itemFlexGridSizer3->Add(

m_LinkageEvidence

, 1, wxALIGN_LEFT | wxGROW | wxALIGN_CENTER_VERTICAL |wxALL, 5);

219

wxBoxSizer* itemBoxSizer21 =

new

wxBoxSizer(wxHORIZONTAL);

220

itemBoxSizer2->Add(itemBoxSizer21, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

222

wxButton* itemButton1 =

new

wxButton( itemDialog1, wxID_OK,

_

(

"Accept"

), wxDefaultPosition, wxDefaultSize, 0 );

223

itemBoxSizer21->Add(itemButton1, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

225

wxButton* itemButton2 =

new

wxButton( itemDialog1, wxID_CANCEL,

_

(

"Cancel"

), wxDefaultPosition, wxDefaultSize, 0 );

226

itemBoxSizer21->Add(itemButton2, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

230  int

gap_type =

m_GapType

->GetSelection();

231  if

(gap_type != wxNOT_FOUND)

233  if

(

m_GapType

->GetString(gap_type) ==

_

(

"repeat"

))

238  if

(

m_GapType

->GetString(gap_type) ==

_

(

"scaffold"

) ||

m_GapType

->GetString(gap_type) ==

_

(

"within"

))

286  int

gap_type = objects::CSeq_gap::eType_unknown;

288  int

linkage_evidence = -1;

290  int

gap_type_sel =

m_GapType

->GetSelection();

291  int

linkage_sel =

m_Linkage

->GetSelection();

292  if

(gap_type_sel != wxNOT_FOUND)

294  string

gap_type_str =

m_GapType

->GetString(gap_type_sel).ToStdString();

295  if

(gap_type_str ==

"within"

)

296

gap_type_str =

"scaffold"

;

297  if

(gap_type_str ==

"between"

)

298

gap_type_str =

"contig"

;

300

linkage = objects::CSeq_gap::eLinkage_unlinked;

301  if

( gap_type_str ==

"repeat"

)

303  if

(linkage_sel != wxNOT_FOUND)

305  if

(

m_Linkage

->GetString(linkage_sel) ==

_

(

"Within Scaffolds"

))

307

linkage = objects::CSeq_gap::eLinkage_linked;

312  if

( gap_type_str ==

"scaffold"

)

314

linkage = objects::CSeq_gap::eLinkage_linked;

321  bool

modified(

false

);

334  bool

has_loc(

false

);

337  if

( (*iter)->IsLoc() )

354  if

(delta_i->Empty())

366  if

(linkage_evidence >= 0)

369

link_ev->SetType(linkage_evidence);

376

}

catch

(

CException

) {}

catch

(std::exception ) {}

398  int

gap_type =

m_GapType

->GetSelection();

399  int

linkage =

m_Linkage

->GetSelection();

400  if

(gap_type != wxNOT_FOUND)

402  if

(

m_GapType

->GetString(gap_type) ==

_

(

"repeat"

))

405  if

(linkage != wxNOT_FOUND &&

m_Linkage

->GetString(linkage) ==

_

(

"Within Scaffolds"

))

410  if

(

m_GapType

->GetString(gap_type) ==

_

(

"scaffold"

) ||

m_GapType

->GetString(gap_type) ==

_

(

"within"

))

419  int

gap_type =

m_GapType

->GetSelection();

420  int

linkage =

m_Linkage

->GetSelection();

421  if

(gap_type != wxNOT_FOUND &&

m_GapType

->GetString(gap_type) ==

_

(

"repeat"

) &&

422

linkage != wxNOT_FOUND &&

m_Linkage

->GetString(linkage) ==

_

(

"Within Scaffolds"

))

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

USING_SCOPE(ncbi::objects)

#define ID_ADD_LINKAGE_TO_GAPS_GAP_TYPE

#define ID_ADD_LINKAGE_TO_GAPS_LINKAGE

static bool ShowToolTips()

Should we show tooltips?

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void OnLinkage(wxCommandEvent &event)

void Init()

Initialises member variables.

wxChoice * m_LinkageEvidence

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle tse)

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Add Linkage To Gaps"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 100), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void CreateControls()

Creates the controls and sizers.

void OnGapType(wxCommandEvent &event)

~CAddLinkageToGaps()

Destructor.

CAddLinkageToGaps()

Constructors.

void AddCommand(IEditCommand &command)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

list< pair< string, TEnumValueType > > TValues

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

Set object to copy of another one.

#define ENUM_METHOD_NAME(EnumName)

TSeqPos GetBioseqLength(void) const

bool IsSetInst(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

bool IsInGap(TSeqPos pos) const

true if sequence at 0-based position 'pos' has gap Note: this method is not MT-safe,...

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TLiteral & SetLiteral(void)

Select the variant.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void SetExt(TExt &value)

Assign a value to Ext data member.

const TLiteral & GetLiteral(void) const

Get the variant data.

bool IsSetExt(void) const

extensions for special types Check if a value has been assigned to Ext data member.

TLength GetLength(void) const

Get the Length member data.

bool IsDelta(void) const

Check if variant Delta is selected.

const TExt & GetExt(void) const

Get the Ext member data.

const TDelta & GetDelta(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

list< CRef< CDelta_seq > > Tdata

@ eMol_na

just a nucleic acid

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

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