Search Toolkit Book for CCDSTranslationPanel

#include "cds_translation_panel.hpp"
(Private to src/gui/widgets/edit.)

Inheritance diagram for CCDSTranslationPanel:

Collaboration diagram for CCDSTranslationPanel:

Public Types
enum	{ ID_CCDSTRANSLATIONPANEL = 10079 , ID_CHOICE1 , ID_CHOICE2 , ID_CHECKBOX , ID_COMBOBOX , ID_FORCE_NEAR_BTN , ID_TEXTCTRL27 , ID_PREDICT_INTERVAL , ID_RETRANSLATE_LINK , ID_HYPERLINKCTRL2 , ID_IMPORT_CDS_PROTEIN , ID_RETRANSLATE_ON_OK_BTN , ID_CHECKBOX3 , ID_UPDATE_GENE_SPAN }
	Control identifiers. More...

Public Member Functions
	CCDSTranslationPanel ()
	Constructors. More...

	CCDSTranslationPanel (wxWindow *parent, objects::CSeq_feat &feat, objects::CScope &scope, 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)

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. More...

	~CCDSTranslationPanel ()
	Destructor. More...

void	Init ()
	Initialises member variables. More...

void	CreateControls ()
	Creates the controls and sizers. More...

virtual bool	TransferDataToWindow ()

virtual bool	TransferDataFromWindow ()

void	SetProduct (objects::CSeq_feat &feat)

void	SetProtein (objects::CBioseq &bioseq)

void	OnPredictIntervalHyperlinkClicked (wxHyperlinkEvent &event)
	wxEVT_COMMAND_HYPERLINK event handler for ID_PREDICT_INTERVAL More...

void	OnRetranslateLinkHyperlinkClicked (wxHyperlinkEvent &event)
	wxEVT_COMMAND_HYPERLINK event handler for ID_RETRANSLATE_LINK More...

void	AdjustForStopCodonHyperlinkClicked (wxHyperlinkEvent &event)
	wxEVT_COMMAND_HYPERLINK event handler for ID_HYPERLINKCTRL2 More...

void	OnImportCdsProteinHyperlinkClicked (wxHyperlinkEvent &event)
	wxEVT_COMMAND_HYPERLINK event handler for ID_IMPORT_CDS_PROTEIN More...

void	OnProductChanged (wxCommandEvent &event)

void	OnRetranslateOnOkChanged (wxCommandEvent &event)

wxBitmap	GetBitmapResource (const wxString &name)
	Retrieves bitmap resources. More...

wxIcon	GetIconResource (const wxString &name)
	Retrieves icon resources. More...

bool	ShouldUpdatemRNALocation ()

bool	ShouldUpdateGeneLocation ()

bool	ShouldRetranslate ()

void	Retranslate ()

bool	ShouldCreateNewProductSeq ()

void	SetProductId (const string &val)

CRef< objects::CSeq_id >	GetProductId ()

void	DisableRetranslateOnOk (bool exception, bool pseudo)

void	UpdateForceNear ()

IRegSettings interface implementation
virtual void	SetRegistryPath (const string &reg_path)

virtual void	LoadSettings ()

virtual void	SaveSettings () const

Public Member Functions inherited from IRegSettings
virtual	~IRegSettings ()

Static Public Member Functions
static bool	ShowToolTips ()
	Should we show tooltips? More...

static bool	IsValidException (const string &text)

Public Attributes
wxChoice *	m_GeneticCode

wxChoice *	m_Frame

wxCheckBox *	m_ConflictCtrl

wxStaticText *	m_ProteinLengthTxt

wxOwnerDrawnComboBox *	m_ProductCtrl

wxCheckBox *	m_ForceNear

wxTextCtrl *	m_TranslationCtrl

wxHyperlinkCtrl *	m_RetranslateLink

wxCheckBox *	m_RetranslateOnOkBtn

wxCheckBox *	m_UpdatemRNASpan

wxCheckBox *	m_UpdateGeneSpan

CRef< objects::CSeq_feat >	m_EditedFeat

objects::CScope *	m_Scope

CRef< objects::CBioseq >	m_EditedBioseq

Private Member Functions
wxTreebook *	x_GetTree ()

bool	x_IsPseudo ()

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

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

bool	x_CollectData ()

void	x_NormalizeGeneticCodeName (string &code_name)

void	x_Translate (void)

void	x_UpdateForceNear (const string &val)

Private Attributes
bool	m_add_stop_codon

string	m_RegPath

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

Detailed Description

CCDSTranslationPanel class declaration

Definition at line 81 of file cds_translation_panel.hpp.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

Control identifiers.

Enumerator
ID_CCDSTRANSLATIONPANEL
ID_CHOICE1
ID_CHOICE2
ID_CHECKBOX
ID_COMBOBOX
ID_FORCE_NEAR_BTN
ID_TEXTCTRL27
ID_PREDICT_INTERVAL
ID_RETRANSLATE_LINK
ID_HYPERLINKCTRL2
ID_IMPORT_CDS_PROTEIN
ID_RETRANSLATE_ON_OK_BTN
ID_CHECKBOX3
ID_UPDATE_GENE_SPAN

Definition at line 163 of file cds_translation_panel.hpp.

Constructor & Destructor Documentation

◆ CCDSTranslationPanel() [1/2]

CCDSTranslationPanel::CCDSTranslationPanel ( )

Constructors.

CCDSTranslationPanel type definition

CCDSTranslationPanel event table definition

CCDSTranslationPanel constructors

Definition at line 143 of file cds_translation_panel.cpp.

References Init().

◆ CCDSTranslationPanel() [2/2]

CCDSTranslationPanel::CCDSTranslationPanel	(	wxWindow *	parent,
		objects::CSeq_feat &	feat,
		objects::CScope &	scope,
		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`
	)

◆ ~CCDSTranslationPanel()

CCDSTranslationPanel::~CCDSTranslationPanel ( )

Destructor.

CCDSTranslationPanel destructor

Definition at line 228 of file cds_translation_panel.cpp.

References SaveSettings().

Member Function Documentation

◆ AdjustForStopCodonHyperlinkClicked()

void CCDSTranslationPanel::AdjustForStopCodonHyperlinkClicked ( wxHyperlinkEvent & event )

wxEVT_COMMAND_HYPERLINK event handler for ID_HYPERLINKCTRL2

Definition at line 1100 of file cds_translation_panel.cpp.

References CSeq_loc::Assign(), eExtreme_Biological, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eNa_strand_minus, ExtendToStopCodon(), NStr::Find(), CBioseq_Handle::GetInst_Length(), CLocationPanel::GetSeq_loc(), CSeq_loc::GetStrand(), i, m_EditedFeat, m_Scope, NULL, CRef< C, Locker >::Reset(), SeqLocExtend(), CCDSExceptionPanel::SetExceptions(), CSeq_loc::SetPartialStop(), CLocationPanel::SetSeq_loc(), CCDSExceptionPanel::TransferDataFromWindow(), TransferDataFromWindow(), CLocationPanel::TransferDataFromWindow(), TransferDataToWindow(), CSeqTranslator::Translate(), TruncateSeqLoc(), wxT, and x_Translate().

◆ Create()

bool CCDSTranslationPanel::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.

CCDSTranslationPanel creator

Definition at line 202 of file cds_translation_panel.cpp.

References _, CreateControls(), m_ProductCtrl, and ncbi::grid::netcache::search::fields::size.

◆ CreateControls()

void CCDSTranslationPanel::CreateControls ( )

Creates the controls and sizers.

Control creation for CCDSTranslationPanel

Definition at line 262 of file cds_translation_panel.cpp.

References _, DisableRetranslateOnOk(), CScope::eAllTSEs, CSeq_id::eFasta, eGetId_Best, CSeq_inst_Base::eMol_aa, CGenetic_code_table_Base::Get(), CGen_code_table::GetCodeTable(), GetId(), CSeq_id::GetLabel(), ID_CHECKBOX, ID_CHECKBOX3, ID_CHOICE1, ID_CHOICE2, ID_COMBOBOX, ID_FORCE_NEAR_BTN, ID_HYPERLINKCTRL2, ID_IMPORT_CDS_PROTEIN, ID_PREDICT_INTERVAL, ID_RETRANSLATE_LINK, ID_RETRANSLATE_ON_OK_BTN, ID_TEXTCTRL27, ID_UPDATE_GENE_SPAN, IsValidException(), ITERATE, label, m_ConflictCtrl, m_EditedFeat, m_ForceNear, m_Frame, m_GeneticCode, m_ProductCtrl, m_ProteinLengthTxt, m_RetranslateLink, m_RetranslateOnOkBtn, m_Scope, m_SeqIds, m_TranslationCtrl, m_UpdateGeneSpan, m_UpdatemRNASpan, ShowToolTips(), str(), ToWxString(), x_IsPseudo(), and x_NormalizeGeneticCodeName().

Referenced by Create().

◆ DisableRetranslateOnOk()

void CCDSTranslationPanel::DisableRetranslateOnOk	(	bool	exception,
		bool	pseudo
	)

Definition at line 390 of file cds_translation_panel.cpp.

References m_RetranslateOnOkBtn.

Referenced by CreateControls(), and CGenericPropsPanel::x_UpdateDisableOnRetranslate().

◆ GetBitmapResource()

wxBitmap CCDSTranslationPanel::GetBitmapResource ( const wxString & name )

Retrieves bitmap resources.

Get bitmap resources

Definition at line 690 of file cds_translation_panel.cpp.

◆ GetIconResource()

wxIcon CCDSTranslationPanel::GetIconResource ( const wxString & name )

Retrieves icon resources.

Get icon resources

Definition at line 703 of file cds_translation_panel.cpp.

◆ GetProductId()

CRef< CSeq_id > CCDSTranslationPanel::GetProductId ( void )

Definition at line 813 of file cds_translation_panel.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), CSeq_id::fParse_Default, NStr::IsBlank(), m_ProductCtrl, m_SeqIds, NULL, CSeq_id_Base::Reset(), NStr::SplitInTwo(), NStr::StartsWith(), tag, ToStdString(), and NStr::TrimPrefixInPlace().

Referenced by SetProductId(), x_CollectData(), and CEditObjectSeq_feat::x_HandleCdsProduct().

◆ Init()

void CCDSTranslationPanel::Init ( void )

Initialises member variables.

Member initialisation

Definition at line 240 of file cds_translation_panel.cpp.

References m_ConflictCtrl, m_ForceNear, m_Frame, m_GeneticCode, m_ProductCtrl, m_ProteinLengthTxt, m_RetranslateLink, m_RetranslateOnOkBtn, m_TranslationCtrl, m_UpdateGeneSpan, m_UpdatemRNASpan, and NULL.

◆ IsValidException()

bool CCDSTranslationPanel::IsValidException ( const string & text )

static

Definition at line 95 of file cds_translation_panel.cpp.

References NON_CONST_ITERATE, NStr::Split(), text(), and NStr::TruncateSpacesInPlace().

Referenced by CreateControls(), x_SetProtein(), and CGenericPropsPanel::x_UpdateDisableOnRetranslate().

◆ LoadSettings()

void CCDSTranslationPanel::LoadSettings ( )

virtual

Implements IRegSettings.

Definition at line 187 of file cds_translation_panel.cpp.

References CRegistryReadView::GetBool(), CGuiRegistry::GetInstance(), CGuiRegistry::GetReadView(), kUpdateGeneSpan, m_RegPath, and m_UpdateGeneSpan.

◆ OnImportCdsProteinHyperlinkClicked()

void CCDSTranslationPanel::OnImportCdsProteinHyperlinkClicked ( wxHyperlinkEvent & event )

wxEVT_COMMAND_HYPERLINK event handler for ID_IMPORT_CDS_PROTEIN

Definition at line 1417 of file cds_translation_panel.cpp.

References GetBioseqHandleForMultihomeLocation(), COpenObjectsDlg::GetObjectLoader(), CRef< C, Locker >::GetPointer(), CSeq_entry_Base::GetSeq(), CTSE_Handle::GetTopLevelEntry(), CBioseq_Handle::GetTSE_Handle(), GUI_AsyncExecUnit(), CBioseq::IsAa(), CSeq_entry_Base::IsSeq(), ITERATE, m_EditedFeat, m_Scope, NULL, IExecuteUnit::PostExecute(), IExecuteUnit::PreExecute(), COpenObjectsDlg::SetManagers(), CDialog::SetRegistryPath(), wxT, and x_SetProtein().

◆ OnPredictIntervalHyperlinkClicked()

void CCDSTranslationPanel::OnPredictIntervalHyperlinkClicked ( wxHyperlinkEvent & event )

wxEVT_COMMAND_HYPERLINK event handler for ID_PREDICT_INTERVAL

Definition at line 1483 of file cds_translation_panel.cpp.

References GetBioseqHandleForMultihomeLocation(), CTSE_Handle::GetTopLevelEntry(), CBioseq_Handle::GetTSE_Handle(), m_EditedFeat, m_Scope, TransferDataToWindow(), and x_SetLocationForProtein().

◆ OnProductChanged()

void CCDSTranslationPanel::OnProductChanged ( wxCommandEvent & event )

Definition at line 1491 of file cds_translation_panel.cpp.

References UpdateForceNear().

◆ OnRetranslateLinkHyperlinkClicked()

void CCDSTranslationPanel::OnRetranslateLinkHyperlinkClicked ( wxHyperlinkEvent & event )

wxEVT_COMMAND_HYPERLINK event handler for ID_RETRANSLATE_LINK

wxEVT_COMMAND_HYPERLINK event handler for ID_HYPERLINKCTRL1

Definition at line 851 of file cds_translation_panel.cpp.

References _, i, CGenericPropsPanel::ResetPseudo(), Retranslate(), wxT, x_GetTree(), and x_IsPseudo().

◆ OnRetranslateOnOkChanged()

void CCDSTranslationPanel::OnRetranslateOnOkChanged ( wxCommandEvent & event )

Definition at line 1526 of file cds_translation_panel.cpp.

References NStr::IsBlank(), m_RetranslateOnOkBtn, m_TranslationCtrl, ToStdString(), wxT, and x_IsPseudo().

◆ Retranslate()

void CCDSTranslationPanel::Retranslate ( )

Definition at line 713 of file cds_translation_panel.cpp.

References CLocationPanel::GetSeq_loc(), i, m_EditedFeat, CCDSExceptionPanel::SetExceptions(), CCDSExceptionPanel::TransferDataFromWindow(), CLocationPanel::TransferDataFromWindow(), TransferDataToWindow(), x_CollectData(), and x_Translate().

Referenced by OnRetranslateLinkHyperlinkClicked(), and CEditObjectSeq_feat::x_HandleCdsProduct().

◆ SaveSettings()

void CCDSTranslationPanel::SaveSettings ( ) const

virtual

Implements IRegSettings.

Definition at line 176 of file cds_translation_panel.cpp.

References CGuiRegistry::GetInstance(), CGuiRegistry::GetWriteView(), kUpdateGeneSpan, m_RegPath, m_UpdateGeneSpan, and CRegistryWriteView::Set().

Referenced by ~CCDSTranslationPanel().

◆ SetProduct()

void CCDSTranslationPanel::SetProduct ( objects::CSeq_feat & feat )

◆ SetProductId()

void CCDSTranslationPanel::SetProductId ( const string & val )

Definition at line 797 of file cds_translation_panel.cpp.

References GetProductId(), m_EditedBioseq, m_EditedFeat, m_ProductCtrl, ToWxString(), val, and x_UpdateForceNear().

Referenced by CEditObjectSeq_feat::x_HandleCdsProduct().

◆ SetProtein()

void CCDSTranslationPanel::SetProtein ( objects::CBioseq & bioseq )

Definition at line 658 of file cds_translation_panel.cpp.

References CSeq_id::Assign(), CSerialObject::Assign(), m_EditedBioseq, CBioseq_Base::ResetInst(), CBioseq_Base::SetId(), CBioseq_Base::SetInst(), and TransferDataFromWindow().

Referenced by CEditObjectSeq_feat::x_HandleCdsProduct().

◆ SetRegistryPath()

void CCDSTranslationPanel::SetRegistryPath ( const string & reg_path )

virtual

Implements IRegSettings.

Definition at line 171 of file cds_translation_panel.cpp.

References m_RegPath.

◆ ShouldCreateNewProductSeq()

bool CCDSTranslationPanel::ShouldCreateNewProductSeq ( )

Definition at line 791 of file cds_translation_panel.cpp.

References m_ForceNear.

Referenced by CEditObjectSeq_feat::x_HandleCdsProduct().

◆ ShouldRetranslate()

bool CCDSTranslationPanel::ShouldRetranslate ( )

inline

Definition at line 186 of file cds_translation_panel.hpp.

References m_RetranslateOnOkBtn.

Referenced by CEditObjectSeq_feat::x_HandleCdsProduct().

◆ ShouldUpdateGeneLocation()

bool CCDSTranslationPanel::ShouldUpdateGeneLocation ( )

inline

Definition at line 185 of file cds_translation_panel.hpp.

References m_UpdateGeneSpan.

Referenced by CEditObjectSeq_feat::x_AdjustGene().

◆ ShouldUpdatemRNALocation()

bool CCDSTranslationPanel::ShouldUpdatemRNALocation ( )

inline

Definition at line 184 of file cds_translation_panel.hpp.

References m_UpdatemRNASpan.

Referenced by CEditObjectSeq_feat::x_UpdatemRNA().

◆ ShowToolTips()

bool CCDSTranslationPanel::ShowToolTips ( )

static

Should we show tooltips?

Definition at line 681 of file cds_translation_panel.cpp.

Referenced by CreateControls().

◆ TransferDataFromWindow()

bool CCDSTranslationPanel::TransferDataFromWindow ( )

virtual

Definition at line 612 of file cds_translation_panel.cpp.

References x_CollectData().

Referenced by AdjustForStopCodonHyperlinkClicked(), SetProtein(), and CEditObjectSeq_feat::x_HandleCdsProduct().

◆ TransferDataToWindow()

bool CCDSTranslationPanel::TransferDataToWindow ( )

virtual

Definition at line 407 of file cds_translation_panel.cpp.

References CSeq_data_Base::e_Ncbieaa, CSeq_id::eFasta, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, eGetId_Best, NStr::EqualCase(), CGenetic_code_table_Base::Get(), CCdregion_Base::GetCode(), CGen_code_table::GetCodeTable(), CCdregion_Base::GetConflict(), CCdregion_Base::GetFrame(), GetId(), CSeq_id::GetLabel(), CSeqVector::GetSeqData(), NStr::IsBlank(), CSeq_id_Base::IsGi(), CCdregion_Base::IsSetCode(), CCdregion_Base::IsSetConflict(), CCdregion_Base::IsSetFrame(), ITERATE, label, m_add_stop_codon, m_ConflictCtrl, m_EditedBioseq, m_EditedFeat, m_Frame, m_GeneticCode, m_ProductCtrl, m_ProteinLengthTxt, m_Scope, m_TranslationCtrl, NcbiWarningBox(), NStr::NumericToString(), CSeqVector::SetCoding(), CSeqVector::size(), str(), ToWxString(), x_NormalizeGeneticCodeName(), and x_UpdateForceNear().

Referenced by AdjustForStopCodonHyperlinkClicked(), OnPredictIntervalHyperlinkClicked(), Retranslate(), and x_SetProtein().

◆ UpdateForceNear()

void CCDSTranslationPanel::UpdateForceNear ( )

Definition at line 1496 of file cds_translation_panel.cpp.

References m_ProductCtrl, ToStdString(), val, and x_UpdateForceNear().

Referenced by OnProductChanged(), and CGenericPropsPanel::x_UpdateDisableOnRetranslate().

◆ x_CollectData()

bool CCDSTranslationPanel::x_CollectData ( )

private

Definition at line 553 of file cds_translation_panel.cpp.

References CCdregion_Base::eFrame_one, CCdregion_Base::eFrame_three, CCdregion_Base::eFrame_two, GetProductId(), NStr::IsBlank(), m_ConflictCtrl, m_EditedBioseq, m_EditedFeat, m_Frame, m_GeneticCode, m_ProductCtrl, CCdregion_Base::ResetConflict(), CCdregion_Base::ResetFrame(), CCdregion_Base::SetCode(), CCdregion_Base::SetConflict(), CCdregion_Base::SetFrame(), and ToStdString().

Referenced by Retranslate(), and TransferDataFromWindow().

◆ x_GetTree()

wxTreebook * CCDSTranslationPanel::x_GetTree ( )

private

Definition at line 519 of file cds_translation_panel.cpp.

References NULL.

Referenced by OnRetranslateLinkHyperlinkClicked(), and x_IsPseudo().

◆ x_IsPseudo()

bool CCDSTranslationPanel::x_IsPseudo ( )

private

Definition at line 534 of file cds_translation_panel.cpp.

References i, CGenericPropsPanel::IsPseudo(), IsPseudo(), m_EditedFeat, m_Scope, and x_GetTree().

Referenced by CreateControls(), OnRetranslateLinkHyperlinkClicked(), OnRetranslateOnOkChanged(), x_Translate(), and x_UpdateForceNear().

◆ x_NormalizeGeneticCodeName()

void CCDSTranslationPanel::x_NormalizeGeneticCodeName ( string & code_name )

private

Definition at line 400 of file cds_translation_panel.cpp.

Referenced by CreateControls(), and TransferDataToWindow().

◆ x_SetLocationForProtein()

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

private

Definition at line 1217 of file cds_translation_panel.cpp.

References CScope::AddTopLevelSeqEntry(), CSeq_id::Assign(), CSeq_loc::Assign(), CSerialObject::Assign(), eExtreme_Biological, CSeq_id::eFasta, CScope::eMissing_Null, CProSplignOutputOptions::ePassThrough, Error(), CProSplign::FindAlignment(), CSeq_loc_mix_Base::Get(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSpliced_seg_Base::GetExons(), CSpliced_seg_Base::GetGenomic_strand(), CSeq_loc::GetId(), CBioseq_Handle::GetInst_Length(), CSeq_feat_Base::GetLocation(), CSeq_loc_Base::GetMix(), CSpliced_seg_Base::GetModifiers(), CException::GetMsg(), CSeq_entry_Handle::GetScope(), CSeq_align_Base::GetSegs(), CBioseq_Handle::GetSeqId(), CSeq_align_Base::C_Segs::GetSpliced(), i, CSeq_loc_Base::IsMix(), CSpliced_seg_Base::IsSetGenomic_strand(), CSeq_align_Base::IsSetSegs(), CSeq_align_Base::C_Segs::IsSpliced(), ITERATE, label, len, LOG_POST, m_EditedBioseq, m_EditedFeat, NULL, CScope::RemoveTopLevelSeqEntry(), CRef< C, Locker >::Reset(), s_ExtendIntervalToEnd(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), CSeq_entry_Base::SetSeq(), CLocationPanel::SetSeq_loc(), CSeq_loc::SetStrand(), ToWxString(), CException::what(), and wxT.

Referenced by OnPredictIntervalHyperlinkClicked().

◆ x_SetProtein()

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

private

◆ x_Translate()

void CCDSTranslationPanel::x_Translate ( void )

private

Definition at line 751 of file cds_translation_panel.cpp.

References CSeq_inst_Base::eMol_aa, NStr::EndsWith(), CSeq_inst_Base::eRepr_raw, m_add_stop_codon, m_EditedBioseq, m_EditedFeat, m_Scope, prot, CRef< C, Locker >::Reset(), CSeqTranslator::Translate(), and x_IsPseudo().

Referenced by AdjustForStopCodonHyperlinkClicked(), and Retranslate().

◆ x_UpdateForceNear()

void CCDSTranslationPanel::x_UpdateForceNear ( const string & val )

private

Definition at line 1502 of file cds_translation_panel.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), NStr::IsBlank(), m_ForceNear, m_SeqIds, val, and x_IsPseudo().

Referenced by SetProductId(), TransferDataToWindow(), and UpdateForceNear().

Member Data Documentation

◆ m_add_stop_codon

bool CCDSTranslationPanel::m_add_stop_codon

private

Definition at line 212 of file cds_translation_panel.hpp.

Referenced by TransferDataToWindow(), x_SetProtein(), and x_Translate().

◆ m_ConflictCtrl

wxCheckBox* CCDSTranslationPanel::m_ConflictCtrl

Definition at line 153 of file cds_translation_panel.hpp.

Referenced by CreateControls(), Init(), TransferDataToWindow(), and x_CollectData().

◆ m_EditedBioseq

CRef<objects::CBioseq> CCDSTranslationPanel::m_EditedBioseq

Definition at line 182 of file cds_translation_panel.hpp.

Referenced by SetProductId(), SetProtein(), TransferDataToWindow(), x_CollectData(), x_SetLocationForProtein(), x_SetProtein(), and x_Translate().

◆ m_EditedFeat

CRef<objects::CSeq_feat> CCDSTranslationPanel::m_EditedFeat

Definition at line 180 of file cds_translation_panel.hpp.

Referenced by AdjustForStopCodonHyperlinkClicked(), CreateControls(), OnImportCdsProteinHyperlinkClicked(), OnPredictIntervalHyperlinkClicked(), Retranslate(), SetProduct(), SetProductId(), TransferDataToWindow(), x_CollectData(), x_IsPseudo(), x_SetLocationForProtein(), and x_Translate().

◆ m_ForceNear

wxCheckBox* CCDSTranslationPanel::m_ForceNear

Definition at line 156 of file cds_translation_panel.hpp.

Referenced by CreateControls(), Init(), ShouldCreateNewProductSeq(), and x_UpdateForceNear().

◆ m_Frame

wxChoice* CCDSTranslationPanel::m_Frame

Definition at line 152 of file cds_translation_panel.hpp.

Referenced by CreateControls(), Init(), TransferDataToWindow(), and x_CollectData().

◆ m_GeneticCode

wxChoice* CCDSTranslationPanel::m_GeneticCode

Definition at line 151 of file cds_translation_panel.hpp.

Referenced by CreateControls(), Init(), TransferDataToWindow(), and x_CollectData().

◆ m_ProductCtrl

wxOwnerDrawnComboBox* CCDSTranslationPanel::m_ProductCtrl

Definition at line 155 of file cds_translation_panel.hpp.

Referenced by Create(), CreateControls(), GetProductId(), Init(), SetProductId(), TransferDataToWindow(), UpdateForceNear(), and x_CollectData().

◆ m_ProteinLengthTxt

wxStaticText* CCDSTranslationPanel::m_ProteinLengthTxt

Definition at line 154 of file cds_translation_panel.hpp.

Referenced by CreateControls(), Init(), and TransferDataToWindow().

◆ m_RegPath

string CCDSTranslationPanel::m_RegPath

private

Definition at line 213 of file cds_translation_panel.hpp.

Referenced by LoadSettings(), SaveSettings(), and SetRegistryPath().

◆ m_RetranslateLink

wxHyperlinkCtrl* CCDSTranslationPanel::m_RetranslateLink

Definition at line 158 of file cds_translation_panel.hpp.

Referenced by CreateControls(), and Init().

◆ m_RetranslateOnOkBtn

wxCheckBox* CCDSTranslationPanel::m_RetranslateOnOkBtn

Definition at line 159 of file cds_translation_panel.hpp.

Referenced by CreateControls(), DisableRetranslateOnOk(), Init(), OnRetranslateOnOkChanged(), ShouldRetranslate(), and x_SetProtein().

◆ m_Scope

objects::CScope* CCDSTranslationPanel::m_Scope

Definition at line 181 of file cds_translation_panel.hpp.

Referenced by AdjustForStopCodonHyperlinkClicked(), CreateControls(), OnImportCdsProteinHyperlinkClicked(), OnPredictIntervalHyperlinkClicked(), TransferDataToWindow(), x_IsPseudo(), and x_Translate().

◆ m_SeqIds

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

private

Definition at line 214 of file cds_translation_panel.hpp.

Referenced by CreateControls(), GetProductId(), and x_UpdateForceNear().

◆ m_TranslationCtrl

wxTextCtrl* CCDSTranslationPanel::m_TranslationCtrl

Definition at line 157 of file cds_translation_panel.hpp.

Referenced by CreateControls(), Init(), OnRetranslateOnOkChanged(), and TransferDataToWindow().

◆ m_UpdateGeneSpan

wxCheckBox* CCDSTranslationPanel::m_UpdateGeneSpan

Definition at line 161 of file cds_translation_panel.hpp.

Referenced by CreateControls(), Init(), LoadSettings(), SaveSettings(), and ShouldUpdateGeneLocation().

◆ m_UpdatemRNASpan

wxCheckBox* CCDSTranslationPanel::m_UpdatemRNASpan

Definition at line 160 of file cds_translation_panel.hpp.

Referenced by CreateControls(), Init(), and ShouldUpdatemRNALocation().

The documentation for this class was generated from the following files:

src/gui/widgets/edit/cds_translation_panel.hpp
src/gui/widgets/edit/cds_translation_panel.cpp

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

◆ anonymous enum

Constructor & Destructor Documentation

◆ CCDSTranslationPanel() [1/2]

◆ CCDSTranslationPanel() [2/2]

◆ ~CCDSTranslationPanel()

Member Function Documentation

◆ AdjustForStopCodonHyperlinkClicked()

◆ Create()

◆ CreateControls()

◆ DisableRetranslateOnOk()

◆ GetBitmapResource()

◆ GetIconResource()

◆ GetProductId()

◆ Init()

◆ IsValidException()

◆ LoadSettings()

◆ OnImportCdsProteinHyperlinkClicked()

◆ OnPredictIntervalHyperlinkClicked()

◆ OnProductChanged()

◆ OnRetranslateLinkHyperlinkClicked()

◆ OnRetranslateOnOkChanged()

◆ Retranslate()

◆ SaveSettings()

◆ SetProduct()

◆ SetProductId()

◆ SetProtein()

◆ SetRegistryPath()

◆ ShouldCreateNewProductSeq()

◆ ShouldRetranslate()

◆ ShouldUpdateGeneLocation()

◆ ShouldUpdatemRNALocation()

◆ ShowToolTips()

◆ TransferDataFromWindow()

◆ TransferDataToWindow()

◆ UpdateForceNear()

◆ x_CollectData()

◆ x_GetTree()

◆ x_IsPseudo()

◆ x_NormalizeGeneticCodeName()

◆ x_SetLocationForProtein()

◆ x_SetProtein()

◆ x_Translate()

◆ x_UpdateForceNear()

Member Data Documentation

◆ m_add_stop_codon

◆ m_ConflictCtrl

◆ m_EditedBioseq

◆ m_EditedFeat

◆ m_ForceNear

◆ m_Frame

◆ m_GeneticCode

◆ m_ProductCtrl

◆ m_ProteinLengthTxt

◆ m_RegPath

◆ m_RetranslateLink

◆ m_RetranslateOnOkBtn

◆ m_Scope

◆ m_SeqIds

◆ m_TranslationCtrl

◆ m_UpdateGeneSpan

◆ m_UpdatemRNASpan