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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/truncate__cds_8cpp_source.html below:

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

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& cds = fi->GetOriginalFeature();

(fi->GetOriginalFeature().Equals(*new_cds))

->AddCommand(*transl_cmd);

prot_feat_ci(prot_bsh, sel);

name =

+name;

new_prot->

().SetProt().SetName().front() = name;

new_mrna->

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new_gene->

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new_loc->

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this_len = it.GetRange().GetLength();

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len_wanted = new_len -

;

(len_wanted == 1) {

new_loc->

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new_loc->

(*partial_loc);

(pos != string::npos) {

((*it)->IsMolinfo())

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@ eExtreme_Biological

5' and 3'

bool TruncateCDSAtStop(CSeq_feat &cds, CScope &scope)

TruncateCDSAtStop A function to truncate a CDS location after the first stop codon in the protein tra...

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

void AddCommand(IEditCommand &command)

namespace ncbi::objects::

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

wxCheckBox * m_TrimProtFeats

void TruncateProteinFeat(objects::CSeq_feat &prot_feat, const objects::CSeq_feat &cds, objects::CScope &scope)

static bool ShowToolTips()

Should we show tooltips?

wxCheckBox * m_Retranslate

wxCheckBox * m_PrependProtName

~CTruncateCDS()

Destructor.

CRef< CCmdComposite > GetCommand()

void AdjustMolinfo(const objects::CSeq_entry &se, CRef< CCmdComposite > composite, const objects::CSeq_feat &cds)

CTruncateCDS()

Constructors.

wxCheckBox * m_ResetGenes

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

void CreateControls()

Creates the controls and sizers.

wxCheckBox * m_TruncateMRNA

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void Init()

Initialises member variables.

bool Create(wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Truncate CDS"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(200, 100), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

objects::CSeq_entry_Handle m_TopSeqEntry

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.

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

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

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.

const CSeq_id * GetId(void) const

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

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

bool AdjustProteinMolInfoToMatchCDS(CMolInfo &molinfo, const CSeq_feat &cds)

AdjustProteinMolInfoToMatchCDS A function to change an existing MolInfo to match a coding region.

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

CConstRef< CSeq_feat > GetOverlappingGene(const CSeq_loc &loc, CScope &scope, ETransSplicing eTransSplicing=eTransSplicing_Auto)

CConstRef< CSeq_feat > GetmRNAforCDS(const CSeq_feat &cds, CScope &scope)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

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.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

bool IsProtein(void) const

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CScope & GetScope(void) const

Get scope this handle belongs to.

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.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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.

const TName & GetName(void) const

Get the Name member data.

bool IsSetName(void) const

protein name Check if a value has been assigned to Name data member.

void ResetPartial(void)

Reset Partial data member.

bool IsSetData(void) const

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

bool IsProt(void) const

Check if variant Prot is selected.

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.

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.

void SetData(TData &value)

Assign a value to Data data member.

const TProt & GetProt(void) const

Get the variant data.

TMolinfo & SetMolinfo(void)

Select the variant.

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

#define FOR_EACH_SEQDESC_ON_SEQENTRY(Itr, Var)

FOR_EACH_SEQDESC_ON_SEQENTRY EDIT_EACH_SEQDESC_ON_SEQENTRY.

static CRef< CSeq_loc > TruncateSeqLoc(const CSeq_loc &orig_loc, size_t new_len)

CRef< CCmdComposite > GetRetranslateCDSCommand(objects::CScope &scope, const objects::CSeq_feat &cds, bool create_general_only)

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