Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/retranslate__cds_8cpp_source.html below:

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

=

;

any_change =

;

(

->IsSetExcept_text() &&

(

->GetExcept_text(),

) != string::npos)

cds_change =

;

(orig_frame != new_frame) {

transl_change =

;

->AddCommand(*subcmd);

(cds_change || transl_change) {

->AddCommand(*chgFeat);

}

(!

.empty()) {

wxMessageBox(wxString(

),

(

), wxOK | wxICON_ERROR,

);

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR,

);

cds.

().SetWhole().Assign(*new_prot_id);

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);

new_feat->

(prot_feat_ci->GetOriginalFeature());

new_feat->

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

->AddCommand(*chgFeat);

any_actions =

;

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

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

bool TruncateCDSAtStop(CSeq_feat &cds, CScope &scope)

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

CRef< objects::CSeq_id > GetNewProtId(objects::CBioseq_Handle bsh, int &offset, string &id_label, bool general_only)

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

vector< CConstRef< CObject > > GetObjects(objects::CBioseq_Handle bsh)

@ eRetranslateCDSObeyStop

@ eRetranslateCDSChooseFrame

@ eRetranslateCDSIgnoreStopExceptEnd

static CRef< CCmdComposite > GetCommand(objects::CSeq_entry_Handle seh, string title, ERetranslateMethod method, string &error)

void apply(objects::CSeq_entry_Handle seh, ICommandProccessor *cmdProcessor, string title, ERetranslateMethod method)

static CRef< CCmdComposite > RetranslateCDSCommand(CScope &scope, const CSeq_feat &old_cds, CSeq_feat &cds, bool &cds_change, int &offset, bool create_general_only)

namespace ncbi::objects::

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

void RemapOtherProtFeats(const objects::CSeq_feat &old_cds, objects::CSeq_feat &cds, objects::CBioseq_Handle bh, CRef< CCmdComposite > composite, bool &any_actions)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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

Set object to copy of another one.

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

static CCdregion::EFrame FindBestFrame(const CSeq_feat &cds, CScope &scope)

Find "best" frame for a coding region.

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)

bool IsProtein(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

const TInst & GetInst(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.

void SetLocation(TLocation &value)

Assign a value to Location data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetProduct(TProduct &value)

Assign a value to Product 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.

void SetData(TData &value)

Assign a value to Data data member.

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 IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

bool IsSetFrame(void) const

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

@ eFrame_not_set

not set, code uses one

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

USING_SCOPE(ncbi::objects)

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

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

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4