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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/bulkcdsaddpanel_8cpp_source.html below:

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

CBulkCmdPanel::Create( parent,

, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemCBulkCmdPanel1->SetSizer(itemBoxSizer2);

wxFlexGridSizer* itemFlexGridSizer3 =

wxFlexGridSizer(0, 2, 0, 0);

itemBoxSizer2->Add(itemFlexGridSizer3, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText4 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(itemStaticText4, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer3->Add(

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

wxStaticText* itemStaticText6 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(itemStaticText6, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxStaticText* itemStaticText8 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(itemStaticText8, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer3->Add(

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

wxStaticText* itemStaticText10 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(itemStaticText10, 0, wxALIGN_CENTER_HORIZONTAL|wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemFlexGridSizer3->Add(

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

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxBoxSizer* itemBoxSizer4 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer4, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText11 =

wxStaticText( itemCBulkCmdPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer4->Add(itemStaticText11, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxArrayString codonStrings;

codonStrings.Add(

(

));

codonStrings.Add(

(

));

codonStrings.Add(

(

));

codonStrings.Add(

(

));

=

wxChoice( itemCBulkCmdPanel1,

, wxDefaultPosition, wxDefaultSize, codonStrings, 0 );

itemBoxSizer4->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxCheckBox( itemCBulkCmdPanel1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

vector<string> ambig_bioseqs;

objects::CBioseq_CI b_iter(

, objects::CSeq_inst::eMol_na);

( ; b_iter ; ++b_iter )

ambiguous(

);

ambig_bioseqs.push_back(accession);

(!ambig_bioseqs.empty())

report(

);

report_dlg->SetTitle(

(

));

report_dlg->

(wxString(report));

report_dlg->Show(

);

find_best_frame =

;

find_best_frame =

;

cds->SetData().SetCdregion();

cds->SetComment(cds_comment);

cds->SetData().SetCdregion().SetCode(*

);

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

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

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

new_gene->SetPartial(

);

new_mrna->

().SetRna().SetExt().SetName(prot_name);

cds->SetData().SetCdregion().SetFrame(objects::CSeqTranslator::FindBestFrame(*cds, bsh.

(), ambiguous));

cds->SetData().SetCdregion().SetFrame(codon_start);

->SetData().SetProt().SetName().push_back(prot_name);

->SetData().SetProt().SetDesc(prot_desc);

;

;

User-defined methods of the data storage class.

@ eExtreme_Biological

5' and 3'

#define ID_BULKCDSADD_COMMENT

#define ID_BULKCDSADD_GENE

#define ID_BULKCDSADD_PROTEIN_DESC

#define ID_BULKCDSADD_PROTEIN_NAME

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

CRef< CGenetic_code > GetGeneticCodeForBioseq(CBioseq_Handle bh)

GetGeneticCodeForBioseq A function to construct the appropriate CGenetic_code object to use when cons...

static bool ShowToolTips()

Should we show tooltips?

wxTextCtrl * m_GeneSymbol

void CreateControls()

Creates the controls and sizers.

wxTextCtrl * m_ProteinDescription

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

objects::CSeq_entry_Handle m_TopSeqEntry

virtual CRef< CCmdComposite > GetCommand()

wxTextCtrl * m_ProteinName

bool Create(wxWindow *parent, wxWindowID id=10030, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxTAB_TRAVERSAL)

Creation.

void Init()

Initialises member variables.

CBulkCDSAddPanel()

Constructors.

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

~CBulkCDSAddPanel()

Destructor.

bool m_create_general_only

virtual string GetErrorMessage()

void AddOneCmd(const objects::CBioseq_Handle &bsh, CRef< CCmdComposite > cmd, bool &ambiguous)

CBulkLocationPanel * m_Location

bool m_add_location_panel

virtual bool ShouldAddToExisting()

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

void SetText(const wxString &text)

namespace ncbi::objects::

CRef< objects::CSeq_entry > CreateTranslatedProteinSequence(CRef< objects::CSeq_feat > cds, objects::CBioseq_Handle nuc_h, bool create_general_only, int *offset=nullptr)

CRef< objects::CSeq_feat > AddProteinFeatureToProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

static void cleanup(void)

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

CConstRef< CSeq_id > GetSeqId(void) const

@ eContent

Untagged human-readable accession or the like.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

bool IsPartialStop(ESeqLocExtremes ext) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

#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 string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static string ULongToString(unsigned long value, TNumToStringFlags flags=0, int base=10)

Convert unsigned long to string.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

void SetData(TData &value)

Assign a value to Data data member.

@ eFrame_not_set

not set, code uses one

@ eFrame_three

reading frame

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

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

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

string ToStdString(const wxString &s)

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