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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/extend__cds__to__stop_8cpp_source.html below:

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

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemCBulkCmdDlg1->SetSizer(itemBoxSizer2);

=

wxCheckBox( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

=

wxCheckBox( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxCheckBox( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

=

wxCheckBox( itemCBulkCmdDlg1,

,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer2->Add(

, 0, wxALIGN_LEFT|wxALL, 5);

itemBoxSizer2->Add(

, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

modified =

;

& loc = fi->GetLocation();

& cds = fi->GetOriginalFeature();

= orig_len;

vector_loc->

().SetId().Assign(*(loc.

()));

vector_loc->

().SetFrom(0);

usable_size = seq.

();

length = usable_size / 3;

(

= 0;

< length; ++

)

(k = 0; k < 3; ++k, ++start)

extension = ((

+ 1) * 3) -

- 3;

last_interval->

().SetId().Assign(*(this_loc->

()));

->AddCommand(*retranslate);

new_inst->Assign(prot_bsh.

());

(new_inst->IsSetSeq_data())

new_inst->ResetSeq_data();

new_inst->ResetExt();

new_inst->SetRepr(objects::CSeq_inst::eRepr_raw);

new_inst->SetSeq_data().SetNcbieaa().Set(

);

->AddCommand(*chgInst);

->AddCommand(*synch_molinfo);

prot_feat_ci(prot_bsh, sel);

( ; prot_feat_ci; ++prot_feat_ci ) {

new_feat->

().SetInt().SetTo(new_inst->GetLength() - 1);

->AddCommand(*chgFeat);

new_gene->Assign(*gene.GetOriginalSeq_feat());

objects::CSeq_loc& gene_loc = gene.GetLocation();

->Assign(*gene_loc.GetId());

new_gene_loc->SetInt(*new_int);

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

new_mrna->Assign(*mrna.GetOriginalSeq_feat());

objects::CSeq_loc& mrna_loc = mrna.GetLocation();

new_mrna->SetLocation().Assign(*new_loc);

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

CLocalRange< TOffset > TRange

define for the fundamental building block of sequence ranges

bool AdjustProteinFeaturePartialsToMatchCDS(CSeq_feat &new_prot, const CSeq_feat &cds)

AdjustProteinFeaturePartialsToMatchCDS A function to change an existing MolInfo to match a coding reg...

objects::CSeq_entry_Handle m_TopSeqEntry

bool Create(wxWindow *parent, wxWindowID id, const wxString &title, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize, long style=wxDEFAULT_FRAME_STYLE, const wxString &name=wxFrameNameStr)

bool GetTopLevelSeqEntryAndProcessor()

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

CExtendCDSToStop()

Constructors.

virtual CRef< CCmdComposite > GetCommand()

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

wxCheckBox * m_ExtendmRNA

~CExtendCDSToStop()

Destructor.

COkCancelPanel * m_OkCancel

virtual string GetErrorMessage()

void CreateControls()

Creates the controls and sizers.

CRef< CCmdComposite > RetranslateCDSCommand(CScope &scope, CSeq_feat &cds)

void ResetGenes(CRef< CCmdComposite > cmd, const objects::CMappedFeat &feat, CRef< CSeq_loc > add, CScope &scope)

static bool ShowToolTips()

Should we show tooltips?

wxCheckBox * m_ExtendProtFeats

wxCheckBox * m_ResetGenes

void ExtendmRNA(CRef< CCmdComposite > cmd, const objects::CMappedFeat &feat, CRef< CSeq_loc > add, CScope &scope)

wxCheckBox * m_Retranslate

bool Create(wxWindow *parent, wxWindowID id=10268, const wxString &caption=_("Extend Proteins to Stop Codons"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(900, 500), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

void Init()

Initialises member variables.

static const CTrans_table & GetTransTable(int id)

namespace ncbi::objects::

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

char GetCodonResidue(int state) const

static int NextCodonState(int state, unsigned char ch)

IWorkbench is the central interface in the application framework.

USING_SCOPE(ncbi::objects)

unsigned int TSeqPos

Type for sequence locations and lengths.

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

Set object to copy of another one.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

ENa_strand GetStrand(void) const

Get the location's strand.

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CConstRef< CSeq_loc > GetRangeAsSeq_loc(void) const

Get seq-loc for the current iterator position.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

void SetPos(size_t pos)

Set iterator's position.

const CSeq_id * GetId(void) const

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

size_t GetSize(void) const

Get number of ranges.

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

void SetPartialStop(bool val, ESeqLocExtremes ext)

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

CMappedFeat GetBestMrnaForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

CMappedFeat GetBestGeneForCds(const CMappedFeat &cds_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool IsProtein(void) const

TInst_Length GetInst_Length(void) const

const TInst & GetInst(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_feat_Handle & GetSeq_feat_Handle(void) const

Get original feature handle.

const_iterator begin(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetPartial(TPartial value)

Assign a value to Partial data member.

const TLocation & GetLocation(void) const

Get the Location member data.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

const TCode & GetCode(void) const

Get the Code member data.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetFrame(void) const

Check if a value has been assigned to Frame data member.

@ eFrame_three

reading frame

bool CanGetTo(void) const

Check if it is safe to call GetTo method.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

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

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

CRef< CCmdComposite > GetSynchronizeProductMolInfoCommand(objects::CScope &scope, const objects::CSeq_feat &cds)

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