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NCBI C++ ToolKit: src/gui/widgets/edit/cds_translation_panel.cpp Source File

,

,

,

vector<string> exceptions;

(sc_LegalExceptions.find((*it).c_str()) != sc_LegalExceptions.end()) {

wxString& caption,

wxPoint& pos,

wxSize&

,

style ) :

(parent,

, caption, pos,

, style);

SetExtraStyle(wxWS_EX_BLOCK_EVENTS);

wxPanel::Create( parent,

, pos,

, style );

GetSizer()->SetSizeHints(

);

wxBoxSizer* itemBoxSizer2 =

wxBoxSizer(wxVERTICAL);

itemPanel1->SetSizer(itemBoxSizer2);

wxFlexGridSizer* itemFlexGridSizer3 =

wxFlexGridSizer(0, 2, 0, 0);

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

wxStaticText* itemStaticText4 =

wxStaticText( itemPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

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

wxArrayString m_GeneticCodeStrings;

=

wxChoice( itemPanel1,

, wxDefaultPosition, wxDefaultSize, m_GeneticCodeStrings, 0 );

->SetToolTip(

(

));

itemFlexGridSizer3->Add(

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

wxStaticText* itemStaticText6 =

wxStaticText( itemPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

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

wxArrayString m_FrameStrings;

m_FrameStrings.Add(

(

));

m_FrameStrings.Add(

(

));

m_FrameStrings.Add(

(

));

=

wxChoice( itemPanel1,

, wxDefaultPosition, wxDefaultSize, m_FrameStrings, 0 );

->SetToolTip(

(

));

itemFlexGridSizer3->Add(

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

wxStaticText* itemStaticText8 =

wxStaticText( itemPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

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

itemFlexGridSizer3->Add(

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

wxStaticText* itemStaticText10 =

wxStaticText( itemPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

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

=

wxStaticText( itemPanel1, wxID_STATIC, wxEmptyString, wxDefaultPosition, wxDefaultSize, 0 );

itemFlexGridSizer3->Add(

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

wxStaticLine* itemStaticLine12 =

wxStaticLine( itemPanel1, wxID_STATIC, wxDefaultPosition, wxDefaultSize, wxLI_HORIZONTAL );

itemBoxSizer2->Add(itemStaticLine12, 0, wxGROW|wxALL, 5);

wxBoxSizer* itemBoxSizer13 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer13, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxStaticText* itemStaticText14 =

wxStaticText( itemPanel1, wxID_STATIC,

(

), wxDefaultPosition, wxDefaultSize, 0 );

itemBoxSizer13->Add(itemStaticText14, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxArrayString m_ProductCtrlStrings;

=

wxOwnerDrawnComboBox( itemPanel1,

, wxEmptyString, wxDefaultPosition, wxDefaultSize, m_ProductCtrlStrings, wxCB_SIMPLE|wxTE_PROCESS_ENTER );

itemBoxSizer13->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer13->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

=

wxTextCtrl( itemPanel1,

, wxEmptyString, wxDefaultPosition, wxSize(400, 100), wxTE_MULTILINE|wxTE_READONLY );

wxBoxSizer* itemBoxSizer18 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer18, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

wxHyperlinkCtrl* itemHyperlinkCtrl19 =

wxHyperlinkCtrl( itemPanel1,

,

(

), wxEmptyString, wxDefaultPosition, wxDefaultSize, wxHL_DEFAULT_STYLE );

itemBoxSizer18->Add(itemHyperlinkCtrl19, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxHyperlinkCtrl* itemHyperlinkCtrl21 =

wxHyperlinkCtrl( itemPanel1,

,

(

), wxEmptyString, wxDefaultPosition, wxDefaultSize, wxHL_DEFAULT_STYLE );

itemHyperlinkCtrl21->SetNormalColour(wxColour(0, 0, 255));

itemHyperlinkCtrl21->SetVisitedColour(wxColour(0, 0, 255));

itemBoxSizer18->Add(itemHyperlinkCtrl21, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxHyperlinkCtrl* itemHyperlinkCtrl22 =

wxHyperlinkCtrl( itemPanel1,

,

(

), wxEmptyString, wxDefaultPosition, wxDefaultSize, wxHL_DEFAULT_STYLE );

itemBoxSizer18->Add(itemHyperlinkCtrl22, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

wxBoxSizer* itemBoxSizer23 =

wxBoxSizer(wxHORIZONTAL);

itemBoxSizer2->Add(itemBoxSizer23, 0, wxALIGN_CENTER_HORIZONTAL|wxALL, 5);

itemBoxSizer23->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

itemBoxSizer23->Add(

, 0, wxALIGN_CENTER_VERTICAL|wxALL, 5);

= (*it)->GetName();

= (*it)->GetId();

string::size_type pos = code_name.find(

);

code_name = (pos != string::npos) ? code_name.substr(0, pos) +

: code_name;

(!wxPanel::TransferDataToWindow()) {

->RemoveFromHistory(prot_bsh);

(feat_seqid_handle)

(

+ seq_label +

+ label_feat +

);

->RemoveFromHistory(bsh);

codeName =

;

codeId =

.GetId();

codeName =

.GetName();

= (*it)->GetName();

= (*it)->GetId();

wxWindow* w = this->GetParent();

wxTreebook* parent =

wxTreebook*

(w);

(

= 0;

< parent->GetPageCount(); ++

) {

(!wxPanel::TransferDataFromWindow()) {

(index != wxNOT_FOUND)

->Set().push_back(ce);

(

->GetSelection ()) {

bioseq.

().push_back(new_id);

wxWindow* parent = this->GetParent();

wxTreebook* tbook =

wxTreebook*

(parent);

(

= 0;

< tbook->GetPageCount(); ++

) {

(!exceptionPanel) {

(locPanel && exceptionPanel) {

(exceptionPanel) {

->SetGeneral().SetDb(db);

->SetGeneral().SetTag().SetStr(

);

->SetLocal().SetStr(id_val);

wxYES == wxMessageBox(

(

),

(

), wxYES_NO | wxICON_QUESTION))

(

= 0;

< parent->GetPageCount(); ++

) {

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

(

+ this_len <= new_len) {

new_loc->

(*this_loc);

new_loc->

(*this_loc);

len_wanted = new_len -

;

(len_wanted == 1) {

partial_loc->

().SetPoint(start);

partial_loc->

().SetTo(start);

partial_loc->

().SetFrom(start);

new_loc->

(*partial_loc);

new_loc->

(*partial_loc);

(pos < loc_start) {

->Assign(*(loc.

()));

}

(pos > loc_stop) {

->Assign(*(loc.

()));

vector_loc->

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

()));

vector_loc->

().SetFrom(0);

vector_loc->

().SetTo(stop +

- 1);

vector_loc->

().SetFrom(stop -

+ 1);

usable_size = seq.

();

length = usable_size / 3;

(

= 0;

< length; ++

) {

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

new_loc->

(*this_loc);

new_loc->

(*this_loc);

extension = ((

+ 1) * 3) -

;

last_interval->

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

()));

new_loc->

(*last_interval);

new_loc->

(*last_interval);

(usable_size < 3 && !new_loc) {

wxWindow* parent = this->GetParent();

wxTreebook* tbook =

wxTreebook*

(parent);

(

= 0;

< tbook->GetPageCount(); ++

) {

(!exceptionPanel) {

(locPanel && exceptionPanel) {

(exceptionPanel) {

(!prot_str.empty()) {

(pos != string::npos) {

len_wanted = 3 * (pos + 1);

(

->GetData().GetCdregion().IsSetFrame()) {

(len_wanted > 0) {

choice = wxMessageBox(

(

),

(

),

wxYES_NO | wxICON_ERROR,

);

(choice == wxYES) {

bsh =

->GetBioseqHandle(*loc);

alignment.

();

(

exception& e) {

alignment.

();

found_start_codon =

;

found_stop_codon =

;

from = (*exon_it)->GetGenomic_start();

(

&ins : insertions)

from = ins.GetTo() + 1;

((*exon_it)->IsSetGenomic_strand()) {

exon2->

((*exon_it)->GetGenomic_strand());

cds_loc->

().Set().push_back(exon2);

((*exon_it)->IsSetGenomic_strand()) {

exon->

((*exon_it)->GetGenomic_strand());

cds_loc->

().Set().push_back(exon);

((*mod_it)->IsStart_codon_found()) {

found_start_codon = (*mod_it)->GetStart_codon_found();

((*mod_it)->IsStop_codon_found()) {

found_stop_codon = (*mod_it)->GetStop_codon_found();

(!cds_loc->

()) {

=

+

+

;

wxOK | wxICON_ERROR,

);

(cds_loc->

().

().size() == 1) {

cds_loc->

(*exon);

(!found_start_codon) {

(found_stop_codon) {

(cds_loc->

()) {

wxWindow* parent = this->GetParent();

wxTreebook* tbook =

wxTreebook*

(parent);

(

= 0;

< tbook->GetPageCount(); ++

) {

(!exceptionPanel) {

(locPanel && exceptionPanel) {

protein_entry->

().

().push_back(product_id);

vector<string> format_ids;

format_ids.push_back(

);

fileManager->LoadFormats(format_ids);

vector<CIRef<IOpenObjectsPanelClient> > loadManagers;

dlg.SetSize(710, 480);

(dlg.ShowModal() == wxID_OK) {

(!object_loader) {

wxMessageBox(

(

),

(

),

wxOK | wxICON_ERROR);

& ptr = obj_it->GetObject();

seq =

*

(&ptr);

(entry && entry->

()) {

seq = &(entry->

());

(seq && seq->

()) {

wxMessageBox(

(

),

(

),

wxOK | wxICON_ERROR);

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR,

);

static CRef< CScope > m_Scope

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

EVT_CHECKBOX(ID_CADJUSTFEATURES_CHECKBOX, CAdjustFeaturesForGaps::OnKnownUnknownSelected) EVT_CHECKBOX(ID_CADJUSTFEATURES_CHECKBOX1

bool GUI_AsyncExecUnit(IExecuteUnit &exec_unit, const wxString &msg)

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

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

CStaticArraySet< const char *, PNocase_CStr > TLegalExceptions

CRef< CSeq_loc > SeqLocExtend(const CSeq_loc &loc, TSeqPos pos, CScope *scope)

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

static CRef< CSeq_loc > ExtendToStopCodon(CRef< CSeq_feat > feat, CScope *scope)

ENa_strand GetStrandForLastInterval(const CSeq_loc &loc)

CBioseq_Handle GetBioseqHandleForMultihomeLocation(CScope &scope, const CSeq_loc &loc)

static void s_ExtendIntervalToEnd(CSeq_interval &ival, size_t len)

DEFINE_STATIC_ARRAY_MAP(TLegalExceptions, sc_LegalExceptions, s_ValidExceptions)

static const char * kUpdateGeneSpan

static const char *const s_ValidExceptions[]

virtual bool TransferDataFromWindow()

void SetExceptions(objects::CCdregion &cds)

void Init()

Initialises member variables.

wxStaticText * m_ProteinLengthTxt

bool Create(wxWindow *parent, wxWindowID id=ID_CCDSTRANSLATIONPANEL, const wxString &caption=_("CDS TranslationPanel"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)

Creation.

virtual bool TransferDataFromWindow()

static bool IsValidException(const string &text)

objects::CScope * m_Scope

void OnProductChanged(wxCommandEvent &event)

void AdjustForStopCodonHyperlinkClicked(wxHyperlinkEvent &event)

wxEVT_COMMAND_HYPERLINK event handler for ID_HYPERLINKCTRL2

void SetProduct(objects::CSeq_feat &feat)

wxBitmap GetBitmapResource(const wxString &name)

Retrieves bitmap resources.

wxTextCtrl * m_TranslationCtrl

virtual void SaveSettings() const

void CreateControls()

Creates the controls and sizers.

void OnRetranslateOnOkChanged(wxCommandEvent &event)

virtual void SetRegistryPath(const string &reg_path)

virtual void LoadSettings()

map< string, CConstRef< objects::CSeq_id > > m_SeqIds

wxOwnerDrawnComboBox * m_ProductCtrl

~CCDSTranslationPanel()

Destructor.

@ ID_RETRANSLATE_ON_OK_BTN

wxIcon GetIconResource(const wxString &name)

Retrieves icon resources.

void x_UpdateForceNear(const string &val)

bool ShouldCreateNewProductSeq()

void OnPredictIntervalHyperlinkClicked(wxHyperlinkEvent &event)

wxEVT_COMMAND_HYPERLINK event handler for ID_PREDICT_INTERVAL

wxCheckBox * m_ConflictCtrl

void SetProtein(objects::CBioseq &bioseq)

void OnRetranslateLinkHyperlinkClicked(wxHyperlinkEvent &event)

wxEVT_COMMAND_HYPERLINK event handler for ID_RETRANSLATE_LINK

void x_NormalizeGeneticCodeName(string &code_name)

wxHyperlinkCtrl * m_RetranslateLink

void x_SetProtein(const objects::CBioseq &protein, CRef< objects::CSeq_feat > cds, objects::CSeq_entry_Handle seh)

CRef< objects::CSeq_feat > m_EditedFeat

wxCheckBox * m_UpdatemRNASpan

void SetProductId(const string &val)

void OnImportCdsProteinHyperlinkClicked(wxHyperlinkEvent &event)

wxEVT_COMMAND_HYPERLINK event handler for ID_IMPORT_CDS_PROTEIN

virtual bool TransferDataToWindow()

CCDSTranslationPanel()

Constructors.

wxCheckBox * m_UpdateGeneSpan

static bool ShowToolTips()

Should we show tooltips?

void DisableRetranslateOnOk(bool exception, bool pseudo)

CRef< objects::CSeq_id > GetProductId()

CRef< objects::CBioseq > m_EditedBioseq

void x_SetLocationForProtein(CRef< objects::CSeq_feat > cds, objects::CSeq_entry_Handle seh)

wxCheckBox * m_RetranslateOnOkBtn

virtual void SetRegistryPath(const string &path)

static const CTrans_table & GetTransTable(int id)

static const CGenetic_code_table & GetCodeTable(void)

CRegistryWriteView GetWriteView(const string &section)

get a read-write view at a particular level.

static CGuiRegistry & GetInstance()

access the application-wide singleton

CRegistryReadView GetReadView(const string &section) const

get a read-only view at a particular level.

void SetSeq_loc(CSerialObject &object)

virtual bool TransferDataFromWindow()

CRef< objects::CSeq_loc > GetSeq_loc() const

IObjectLoader * GetObjectLoader()

void SetManagers(vector< CIRef< IOpenObjectsPanelClient > > &managers)

Output filtering parameters.

@ ePassThrough

all zeroes - no filtering

spliced protein to genomic alignment

CRef< objects::CSeq_align > FindAlignment(objects::CScope &scope, const objects::CSeq_id &protein, const objects::CSeq_loc &genomic, CProSplignOutputOptions output_options=CProSplignOutputOptions())

Aligns protein to a region on genomic sequence.

class CRegistryReadView provides a nested hierarchical view at a particular key.

bool GetBool(const string &key, bool default_val=false) const

void Set(const string &key, int val)

access a named key at this level, with no recursion

SeqMap related exceptions.

namespace ncbi::objects::

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

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

char GetCodonResidue(int state) const

static int NextCodonState(int state, unsigned char ch)

virtual bool PreExecute()=0

virtual bool PostExecute()=0

vector< SObject > TObjects

const_iterator end() const

const_iterator find(const key_type &key) const

static const char * str(char *buf, int n)

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.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

void NcbiWarningBox(const string &message, const string &title="Warning")

specialized Message Box function for reporting non-critical errors

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

Set object to copy of another one.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

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

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

@ fParse_Default

By default in ParseIDs and IsValid, allow raw parsable non-numeric accessions and plausible local acc...

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

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.

CConstRef< CSeq_loc > GetRangeAsSeq_loc(void) const

Get seq-loc for the current iterator position.

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 SetPartialStart(bool val, ESeqLocExtremes ext)

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

ENa_strand GetStrand(void) const

const CSeq_id & GetSeq_id(void) const

Get seq_id of the current location.

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

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,...

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.

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

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

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.

@ eGetId_Best

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

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void RemoveTopLevelSeqEntry(const CTSE_Handle &entry)

Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq().

vector< CSeq_entry_Handle > TTSE_Handles

const CTSE_Handle & GetTSE_Handle(void) const

Get CTSE_Handle of containing TSE.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

bool IsProtein(void) const

TInst_Length GetInst_Length(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

void SetCoding(TCoding coding)

const_iterator begin(void) const

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

Check if a string ends with a specified suffix value.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

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.

static bool EqualCase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-sensitive equality of a substring with another string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static void TrimPrefixInPlace(string &str, const CTempString prefix, ECase use_case=eCase)

Trim prefix from a string (in-place)

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static const char label[]

bool IsSetSegs(void) const

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

TGenomic_strand GetGenomic_strand(void) const

Get the Genomic_strand member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

list< CRef< CSpliced_seg_modifier > > TModifiers

bool IsSetGenomic_strand(void) const

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

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

bool IsSpliced(void) const

Check if variant Spliced is selected.

const TModifiers & GetModifiers(void) const

Get the Modifiers member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

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.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void ResetCode(void)

Reset Code data member.

void SetProduct(TProduct &value)

Assign a value to Product data member.

void SetCode(TCode &value)

Assign a value to Code data member.

list< CRef< CGenetic_code > > Tdata

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsSetConflict(void) const

conflict Check if a value has been assigned to Conflict data member.

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.

void ResetFrame(void)

Reset Frame data member.

void ResetConflict(void)

Reset Conflict data member.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

const TProduct & GetProduct(void) const

Get the Product member data.

const Tdata & Get(void) const

Get the member data.

void ResetProduct(void)

Reset Product data member.

void SetConflict(TConflict value)

Assign a value to Conflict data member.

bool IsSetProduct(void) const

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

void SetFrame(TFrame value)

Assign a value to Frame data member.

TConflict GetConflict(void) const

Get the Conflict member data.

bool IsSetFrame(void) const

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

bool IsSetLocation(void) const

feature made from Check if a value has been assigned to Location data member.

@ eFrame_three

reading frame

void SetTo(TTo value)

Assign a value to To data member.

bool IsMix(void) const

Check if variant Mix is selected.

ENa_strand

strand of nucleic acid

TFrom GetFrom(void) const

Get the From member data.

virtual void Reset(void)

Reset the whole object.

void SetFrom(TFrom value)

Assign a value to From data member.

const Tdata & Get(void) const

Get the member data.

bool IsSetStrand(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

bool IsGi(void) const

Check if variant Gi is selected.

TTo GetTo(void) const

Get the To member data.

const TMix & GetMix(void) const

Get the variant data.

const TSeq & GetSeq(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

TSeq & SetSeq(void)

Select the variant.

TId & SetId(void)

Assign a value to Id data member.

void ResetId(void)

Reset Id data member.

void SetInst(TInst &value)

Assign a value to Inst data member.

void ResetInst(void)

Reset Inst data member.

@ eRepr_raw

continuous sequence

@ e_Ncbieaa

extended ASCII 1 letter aa codes

static void text(MDB_val *v)

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

#define ID_HYPERLINKCTRL2

wxString ToWxString(const string &s)

string ToStdString(const wxString &s)

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