CAlignmentAssistant Class Reference

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#include <gui/widgets/edit/alignment_assistant.hpp>

Inheritance diagram for CAlignmentAssistant:

Collaboration diagram for CAlignmentAssistant:

Public Member Functions
	CAlignmentAssistant ()
	Constructors. More...
	CAlignmentAssistant (wxWindow *parent, CSeq_entry_Handle seh, ICommandProccessor *processor, CConstRef< CSeq_align > align=CConstRef< CSeq_align >(NULL), wxWindowID id=wxID_ANY, const wxString &caption=_("Alignment Assistant"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(775, 595), long style=wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)
bool	Create (wxWindow *parent, wxWindowID id=wxID_ANY, const wxString &caption=_("Alignment Assistant"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(775, 595), long style=wxMINIMIZE_BOX|wxMAXIMIZE_BOX|wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL)
	Creation. More...
virtual	~CAlignmentAssistant ()
	Destructor. More...
void	Init ()
	Initialises member variables. More...
void	CreateControls ()
	Creates the controls and sizers. More...
wxBitmap	GetBitmapResource (const wxString &name)
	Retrieves bitmap resources. More...
wxIcon	GetIconResource (const wxString &name)
	Retrieves icon resources. More...
void	OnClose (wxCommandEvent &event)
void	OnGoTo (wxCommandEvent &event)
void	OnGoToSeq (wxCommandEvent &event)
void	OnFeatures (wxCommandEvent &event)
void	OnSubstitute (wxCommandEvent &event)
void	ReportPos (int pos, const string &label)
void	ReportRange (int pos1, int pos2, const string &label)
void	IsSelectionAndClean (wxUpdateUIEvent &event)
void	IsNucleotide (wxUpdateUIEvent &event)
void	CreateFeature (wxCommandEvent &event)
void	OnTarget (wxCommandEvent &event)
void	OnExportInter (wxCommandEvent &event)
void	OnExportCont (wxCommandEvent &event)
void	OnValidate (wxCommandEvent &event)
void	OnPropagateFeatures (wxCommandEvent &)
void	OnRemoveSeqFromAlign (wxCommandEvent &)
void	OnReverseStrand (wxCommandEvent &)
void	OnAddAlignCDS (wxCommandEvent &)
void	OnAddAlignRNA (wxCommandEvent &)
void	OnAddAlignOther (wxCommandEvent &)
void	TranslateLocations (CRef< CSeq_loc > loc, vector< pair< CRef< CSeq_loc >, CBioseq_Handle > > &locations)
void	DeleteSelection ()
Public Member Functions inherited from CEventHandler
	CEventHandler ()
	CEventHandler. More...
virtual	~CEventHandler ()
virtual void	AddListener (CEventHandler *listener, int pool_name=ePool_Default)
	Add a listener. More...
virtual void	RemoveListener (CEventHandler *listener)
	Remove a listener. More...
virtual void	RemoveAllListeners (void)
virtual bool	HasListener (CEventHandler *listener, int pool_name=ePool_Default) const
	returns "true" if the given listener belongs to the specified pool More...
virtual const TListeners *	GetListeners (int pool_name=ePool_Default) const
	returns a set of listeners fro the specified pool More...
virtual bool	OnEvent (CEvent *evt)
	Processes en event. Returns "true" if event has been processed. More...
virtual bool	Dispatch (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
	Dispatches an event to the listeners (but does not handle it). More...
virtual bool	Send (CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
	Sends an event synchronously. More...
virtual bool	Send (CEvent *evt, int pool_name)
void	Post (CRef< CEvent > evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)
	Handles an event asynchronously (process and/or dispatch). More...

Static Public Member Functions
static bool	ShowToolTips ()
	Should we show tooltips? More...
Static Public Member Functions inherited from CEventHandler
static bool	HandlePostRequest ()
static void	ClearPostQueue ()
	erases all events from the queue More...
static void	DestroyPostQueue ()

Private Member Functions
void	GetFeatures ()
void	GetAlignment (CConstRef< CSeq_align > align)
bool	x_ExecuteCommand (IEditCommand *command)
void	ReportUnresolvedBioseqs (void)
void	AdjustBioseq (CBioseq_Handle bsh, int from, int to, CRef< CCmdComposite > cmd)
CRef< CSeq_align >	AdjustAlign (int from, int to, const vector< int > &offset, CRef< CCmdComposite > cmd)
void	AdjustFeatureLocations (CBioseq_Handle bsh, int from, int to, CRef< CCmdComposite > cmd)
CRef< CSeq_loc >	AdjustLoc (const CSeq_loc &feat_loc, int from, int to, bool &modified, bool &removed)
void	TrimQualityScores (CBioseq_Handle bsh, int from, int to, CRef< CCmdComposite > command)

Private Attributes
CSeq_entry_Handle	m_TopSeqEntry
CSeq_align_Handle	m_Alignment
ICommandProccessor *	m_CmdProcessor
CPaintAlignment *	m_Panel
vector< vector< vector< pair< TSeqPos, TSeqPos > > > >	m_FeatRanges
vector< vector< pair< string, CSeqFeatData::ESubtype > > >	m_FeatTypes
vector< vector< CBioseq_Handle::EVectorStrand > >	m_FeatStrand
wxStaticText *	m_Range
wxTextCtrl *	m_GoTo_TextCtrl
wxTextCtrl *	m_GoToSeq_TextCtrl
bool	m_is_nucleotide
vector< string >	m_Labels
wxMenu *	m_target_submenu

Additional Inherited Members
Public Types inherited from CEventHandler
enum	EDispatch { eDispatch_SelfOnly , eDispatch_AllHandlers , eDispatch_FirstHandler , eDispatch_Default = eDispatch_AllHandlers }
	enum controlling dispatching strategies More...
enum	EPoolName {   ePool_Default = 0 , ePool_Parent , ePool_Child , ePool_Sibling ,   ePool_NextAvailable }
	Identifiers for standard pools. More...
typedef vector< CEventHandler * >	TListeners
typedef map< int, TListeners >	TPools
typedef list< AutoPtr< SPostRequest > >	TPostRequests
typedef std::map< CEventHandler *, int >	THandlerToCount
typedef void(*	FOnPostCallback) ()
Protected Member Functions inherited from CEventHandler
virtual const SEvtMap *	GetEventMap () const
void	x_DeclareDead ()
	Removes itself unavailable for async event delivery. More...
void	x_AddListenerToPool (CEventHandler *listener, int pool_name)
Protected Attributes inherited from CEventHandler
TPools	m_Pools
Static Protected Attributes inherited from CEventHandler
static const SEvtMap	sm_EvtMap

Detailed Description

Definition at line 99 of file alignment_assistant.hpp.

Constructor & Destructor Documentation

CAlignmentAssistant() [1/2]

static CAlignmentAssistant::CAlignmentAssistant

(

)

Constructors.

CAlignmentAssistant event table definition

CAlignmentAssistant constructors

Definition at line 276 of file alignment_assistant.cpp.

References Init().

CAlignmentAssistant() [2/2]

CAlignmentAssistant::CAlignmentAssistant	(	wxWindow *	parent,
		CSeq_entry_Handle	seh,
		ICommandProccessor *	processor,
		CConstRef< CSeq_align >	align = CConstRef<CSeq_align>(NULL),
		wxWindowID	id = wxID_ANY,
		const wxString &	caption = _("Alignment Assistant"),
		const wxPoint &	pos = wxDefaultPosition,
		const wxSize &	size = wxSize(775,595),
		long	style = wxMINIMIZE_BOX | wxMAXIMIZE_BOX |wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL
	)

Definition at line 282 of file alignment_assistant.cpp.

References Create(), GetAlignment(), Init(), ReportUnresolvedBioseqs(), NEditingStats::ReportUsage(), and ncbi::grid::netcache::search::fields::size.

~CAlignmentAssistant()

CAlignmentAssistant::~CAlignmentAssistant ( )

virtual

Destructor.

CAlignmentAssistant destructor

Definition at line 318 of file alignment_assistant.cpp.

Member Function Documentation

AdjustAlign()

CRef< CSeq_align > CAlignmentAssistant::AdjustAlign ( int  from, int  to, const vector< int > &  offset, CRef< CCmdComposite >  cmd  )

private

Definition at line 904 of file alignment_assistant.cpp.

References CSerialObject::Assign(), cmd, eNa_strand_minus, CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Handle::GetSegs(), CSeq_align_Handle::GetSeq_align(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), CDense_seg_Base::IsSetStrands(), ITERATE, len, m_Alignment, offset, CSeq_align_Base::ResetSegs(), CDense_seg_Base::SetDim(), CDense_seg_Base::SetIds(), CDense_seg_Base::SetLens(), CDense_seg_Base::SetNumseg(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), and si.

Referenced by DeleteSelection().

AdjustBioseq()

void CAlignmentAssistant::AdjustBioseq ( CBioseq_Handle  bsh, int  from, int  to, CRef< CCmdComposite >  cmd  )

private

Definition at line 831 of file alignment_assistant.cpp.

References CScope::AddTopLevelSeqEntry(), cmd, copy(), CSeq_data_Base::e_Iupacaa, CSeqUtil::e_Iupacaa, CSeq_data_Base::e_Iupacna, CSeqUtil::e_Iupacna, CSeqMap::fFindData, CSeq_entry_Handle::GetCompleteSeq_entry(), CBioseq_Base::GetInst(), CObjectManager::GetInstance(), CSeqMap_CI::GetLength(), CSeq_entry_Base::GetSeq(), CSeq_entry_Handle::GetSeq(), CBioseq_Handle::GetSeq_entry_Handle(), CSeqMap_I::GetSequence(), CBioseq_Handle::IsNa(), len, CSeqMap_I::Remove(), SSeqMapSelector::SetFlags(), and CSeqMap_I::SetSequence().

Referenced by DeleteSelection().

AdjustFeatureLocations()

void CAlignmentAssistant::AdjustFeatureLocations ( CBioseq_Handle  bsh, int  from, int  to, CRef< CCmdComposite >  cmd  )

private

Definition at line 1143 of file alignment_assistant.cpp.

References AdjustLoc(), CSerialObject::Assign(), cmd, EDIT_EACH_CODEBREAK_ON_CDREGION, eExtreme_Biological, ERASE_CODEBREAK_ON_CDREGION, CTrna_ext_Base::GetAnticodon(), CSeq_feat_Base::GetData(), CRNA_ref_Base::GetExt(), CBioseq_Handle::GetRangeSeq_loc(), CSeqFeatData_Base::GetRna(), CBioseq_Handle::GetScope(), CSeq_loc::GetStart(), CRNA_ref_Base::C_Ext::GetTRNA(), CSeqFeatData_Base::IsCdregion(), CSeqFeatData_Base::IsRna(), CTrna_ext_Base::IsSetAnticodon(), CSeq_feat_Base::IsSetData(), CRNA_ref_Base::IsSetExt(), CRNA_ref_Base::C_Ext::IsTRNA(), CSeq_feat_Base::SetData(), and CSeq_feat_Base::SetLocation().

Referenced by DeleteSelection().

AdjustLoc()

CRef< CSeq_loc > CAlignmentAssistant::AdjustLoc ( const CSeq_loc &  feat_loc, int  from, int  to, bool &  modified, bool &  removed  )

private

Definition at line 1223 of file alignment_assistant.cpp.

References CSeq_loc::Assign(), CSeq_loc_I::Delete(), eExtreme_Positional, CRange_Base::GetFrom(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSize(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CRange_Base::GetTo(), CSeq_loc_I::HasChanges(), CSeq_loc_I::MakeSeq_loc(), CSeq_loc_CI::Rewind(), CSeq_loc_I::SetFrom(), and CSeq_loc_I::SetTo().

Referenced by AdjustFeatureLocations(), and TrimQualityScores().

Create()

bool CAlignmentAssistant::Create	(	wxWindow *	parent,
		wxWindowID	id = wxID_ANY,
		const wxString &	caption = _("Alignment Assistant"),
		const wxPoint &	pos = wxDefaultPosition,
		const wxSize &	size = wxSize(775,595),
		long	style = wxMINIMIZE_BOX | wxMAXIMIZE_BOX |wxCAPTION|wxRESIZE_BORDER|wxSYSTEM_MENU|wxCLOSE_BOX|wxTAB_TRAVERSAL
	)

Creation.

Definition at line 294 of file alignment_assistant.cpp.

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

Referenced by CAlignmentAssistant().

CreateControls()

void CAlignmentAssistant::CreateControls

(

)

Creates the controls and sizers.

Control creation for CAlignmentAssistant

Definition at line 341 of file alignment_assistant.cpp.

References _, CUICommandRegistry::CreateMenu(), CUICommandRegistry::GetInstance(), i, ID_ADD_ALIGN_CDS_ALIGNMENT_ASSISTANT_MENU, ID_ADD_ALIGN_OTHER_ALIGNMENT_ASSISTANT_MENU, ID_ADD_ALIGN_RNA_ALIGNMENT_ASSISTANT_MENU, ID_CLOSE_ALIGNMENT_ASSISTANT_BUTTON, ID_EDIT_PROPAGATE_ALIGNMENT_ASSISTANT_MENU, ID_EDIT_REV_STRANDS_ALIGNMENT_ASSISTANT_MENU, ID_EDIT_RM_SEQ_ALIGNMENT_ASSISTANT_MENU, ID_EDIT_VALIDATE_ALIGNMENT_ASSISTANT_MENU, ID_EXPORT_CONT_ALIGNMENT_ASSISTANT_MENU, ID_EXPORT_INTER_ALIGNMENT_ASSISTANT_MENU, ID_GOTO_ALIGNMENT_ASSISTANT_BUTTON, ID_GOTO_SEQ_ALIGNMENT_ASSISTANT_BUTTON, ID_SHOW_FEATURES_ALIGNMENT_ASSISTANT_MENU, ID_SHOW_SUBSTITUTE_ALIGNMENT_ASSISTANT_MENU, m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_GoTo_TextCtrl, m_GoToSeq_TextCtrl, m_Labels, m_Panel, m_Range, m_target_submenu, OnTarget(), wxID_ANY, and wxT.

Referenced by Create().

CreateFeature()

void CAlignmentAssistant::CreateFeature

(

wxCommandEvent &

event

)

Definition at line 724 of file alignment_assistant.cpp.

References CSeq_loc::Assign(), cmd, eNa_strand_minus, CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), CBioseqEditor::GetFeatTypeFromCmdID(), GetFeatures(), CSeq_loc::GetId(), CBioseq_Handle::GetRangeSeq_loc(), CPaintAlignment::GetRow(), CBioseq_Handle::GetScope(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CPaintAlignment::GetSelection(), CBioseq_Handle::GetSeq_entry_Handle(), CDense_seg::GetSeq_id(), CPaintAlignment::GetVisibleRow(), m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Panel, m_TopSeqEntry, CBioseqEditor::MakeDefaultFeature(), NULL, CEditObjViewDlgModal::SetEditor(), CEditObjViewDlgModal::SetEditorWindow(), CSeq_loc::SetInt(), CSeq_feat_Base::SetLocation(), swap(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

DeleteSelection()

void CAlignmentAssistant::DeleteSelection

(

)

Definition at line 776 of file alignment_assistant.cpp.

References _, AdjustAlign(), AdjustBioseq(), AdjustFeatureLocations(), cmd, GetAlignment(), CPaintAlignment::GetAlignSelection(), CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CPaintAlignment::GetSelection(), CDense_seg::GetSeq_id(), CPaintAlignment::GetTotalLength(), CPaintAlignment::IsSelection(), m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Panel, m_TopSeqEntry, offset, CPaintAlignment::SetAlign(), swap(), TrimQualityScores(), CPaintAlignment::UpdateFeatures(), wxT, and x_ExecuteCommand().

Referenced by CPaintAlignment::OnKeyDown().

GetAlignment()

void CAlignmentAssistant::GetAlignment ( CConstRef< CSeq_align >  align )

private

Definition at line 459 of file alignment_assistant.cpp.

References CSerialObject::Equals(), eUnknown, GetFeatures(), m_Alignment, m_TopSeqEntry, NCBI_THROW, and CSeq_align_Handle::Reset().

Referenced by CAlignmentAssistant(), DeleteSelection(), OnRemoveSeqFromAlign(), and OnReverseStrand().

GetBitmapResource()

wxBitmap CAlignmentAssistant::GetBitmapResource

(

const wxString &

name

)

Retrieves bitmap resources.

Get bitmap resources

Definition at line 493 of file alignment_assistant.cpp.

GetFeatures()

void CAlignmentAssistant::GetFeatures ( )

private

Definition at line 598 of file alignment_assistant.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_loc_CI::eEmpty_Skip, eExtreme_Positional, eNa_strand_minus, CSeq_loc_CI::eOrder_Positional, CBioseq_Handle::eStrand_Minus, CBioseq_Handle::eStrand_Plus, fFGL_Content, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetData(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CRange_Base::GetFrom(), GetLabel(), CMappedFeat::GetLocation(), CDense_seg_Base::GetNumseg(), CMappedFeat::GetOriginalFeature(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CDense_seg::GetSeq_id(), CPaintAlignment::GetSeqTitle(), CSeq_loc::GetStart(), CSeq_loc::GetStrand(), CSeqFeatData::GetSubtype(), CRange_Base::GetTo(), CBioseq_Handle::IsNucleotide(), CSeq_feat_Base::IsSetData(), CDense_seg_Base::IsSetDim(), CDense_seg_Base::IsSetIds(), CDense_seg_Base::IsSetLens(), CDense_seg_Base::IsSetNumseg(), CDense_seg_Base::IsSetStarts(), label, m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_is_nucleotide, m_Labels, and CSeq_align_Base::C_Segs::Which().

Referenced by CreateFeature(), GetAlignment(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), and OnPropagateFeatures().

GetIconResource()

wxIcon CAlignmentAssistant::GetIconResource

(

const wxString &

name

)

Retrieves icon resources.

Get icon resources

Definition at line 504 of file alignment_assistant.cpp.

Init()

void CAlignmentAssistant::Init

(

void

)

Initialises member variables.

Member initialisation

Definition at line 329 of file alignment_assistant.cpp.

References m_GoTo_TextCtrl, m_GoToSeq_TextCtrl, m_Panel, and NULL.

Referenced by CAlignmentAssistant().

IsNucleotide()

void CAlignmentAssistant::IsNucleotide

(

wxUpdateUIEvent &

event

)

Definition at line 718 of file alignment_assistant.cpp.

References m_is_nucleotide, and m_TopSeqEntry.

IsSelectionAndClean()

void CAlignmentAssistant::IsSelectionAndClean

(

wxUpdateUIEvent &

event

)

Definition at line 707 of file alignment_assistant.cpp.

References CSeqFeatData::AllowedFeatureLocation(), CSeqFeatData::eFeatureLocationAllowed_NucOnly, CSeqFeatData::eFeatureLocationAllowed_ProtOnly, CBioseqEditor::GetFeatTypeFromCmdID(), CPaintAlignment::GetVisibleRow(), CPaintAlignment::IsSelection(), m_is_nucleotide, m_Panel, and m_TopSeqEntry.

OnAddAlignCDS()

void CAlignmentAssistant::OnAddAlignCDS

(

wxCommandEvent &

)

Definition at line 1426 of file alignment_assistant.cpp.

References cmd, eNa_strand_minus, CPaintAlignment::GetAlignSelection(), CAlignCDSAddPanel::GetCommand(), GetFeatures(), CSeq_entry_Handle::GetScope(), i, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Labels, m_Panel, m_TopSeqEntry, CSeq_loc::SetInt(), str(), swap(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

OnAddAlignOther()

void CAlignmentAssistant::OnAddAlignOther

(

wxCommandEvent &

)

Definition at line 1506 of file alignment_assistant.cpp.

References cmd, eNa_strand_minus, CPaintAlignment::GetAlignSelection(), CAlignOtherAddPanel::GetCommand(), GetFeatures(), i, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Labels, m_Panel, m_TopSeqEntry, CSeq_loc::SetInt(), str(), swap(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

OnAddAlignRNA()

void CAlignmentAssistant::OnAddAlignRNA

(

wxCommandEvent &

)

Definition at line 1466 of file alignment_assistant.cpp.

References cmd, eNa_strand_minus, CPaintAlignment::GetAlignSelection(), CAlignRNAAddPanel::GetCommand(), GetFeatures(), CSeq_entry_Handle::GetScope(), i, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Labels, m_Panel, m_TopSeqEntry, CSeq_loc::SetInt(), str(), swap(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

OnClose()

void CAlignmentAssistant::OnClose

(

wxCommandEvent &

event

)

Definition at line 512 of file alignment_assistant.cpp.

OnExportCont()

void CAlignmentAssistant::OnExportCont

(

wxCommandEvent &

event

)

Definition at line 1657 of file alignment_assistant.cpp.

References CFileExtensions::GetDialogFilter(), CPaintAlignment::GetExportCont(), CFileExtensions::kAllFiles, m_Panel, out(), and wxT.

OnExportInter()

void CAlignmentAssistant::OnExportInter

(

wxCommandEvent &

event

)

Definition at line 1638 of file alignment_assistant.cpp.

References CFileExtensions::GetDialogFilter(), CPaintAlignment::GetExportInter(), CFileExtensions::kAllFiles, m_Panel, out(), and wxT.

OnFeatures()

void CAlignmentAssistant::OnFeatures

(

wxCommandEvent &

event

)

Definition at line 677 of file alignment_assistant.cpp.

References CPaintAlignment::EnableFeatures(), and m_Panel.

OnGoTo()

void CAlignmentAssistant::OnGoTo

(

wxCommandEvent &

event

)

Definition at line 537 of file alignment_assistant.cpp.

References m_GoTo_TextCtrl, m_Panel, CPaintAlignment::SetPos(), and val.

OnGoToSeq()

void CAlignmentAssistant::OnGoToSeq

(

wxCommandEvent &

event

)

Definition at line 548 of file alignment_assistant.cpp.

References m_GoToSeq_TextCtrl, m_Panel, CPaintAlignment::SetPosSeq(), and val.

OnPropagateFeatures()

void CAlignmentAssistant::OnPropagateFeatures

(

wxCommandEvent &

)

Definition at line 1707 of file alignment_assistant.cpp.

References cmd, CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), GetFeatures(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CDense_seg::GetSeq_id(), CPaintAlignment::GetTarget(), m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Panel, NULL, CEditObjViewDlgModal::SetEditor(), CEditObjViewDlgModal::SetEditorWindow(), CPaintAlignment::UpdateFeatures(), and x_ExecuteCommand().

OnRemoveSeqFromAlign()

void CAlignmentAssistant::OnRemoveSeqFromAlign

(

wxCommandEvent &

)

Definition at line 1748 of file alignment_assistant.cpp.

References _, CSerialObject::Assign(), cmd, GetAlignment(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetIds(), CDense_seg_Base::GetNumseg(), CSeq_align_Base::GetSegs(), CSeq_align_Handle::GetSeq_align(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), CPaintAlignment::GetTarget(), i, CDense_seg_Base::IsSetNumseg(), CDense_seg_Base::IsSetStarts(), CDense_seg_Base::IsSetStrands(), m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Labels, m_Panel, m_target_submenu, CPaintAlignment::RefreshWithScroll(), CPaintAlignment::SetAlign(), CSeq_align_Base::SetDim(), CSeq_align_Base::SetSegs(), CPaintAlignment::UpdateFeatures(), wxT, and x_ExecuteCommand().

OnReverseStrand()

void CAlignmentAssistant::OnReverseStrand

(

wxCommandEvent &

)

Definition at line 1838 of file alignment_assistant.cpp.

References _, CSerialObject::Assign(), cmd, eNa_strand_minus, eNa_strand_plus, GetAlignment(), CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSeq_align(), CDense_seg::GetSeq_id(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), CPaintAlignment::GetTarget(), CDense_seg_Base::IsSetStrands(), len, m_Alignment, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_Panel, CPaintAlignment::RefreshWithScroll(), CPaintAlignment::SetAlign(), CSeq_align_Base::SetSegs(), CDense_seg_Base::SetStarts(), CDense_seg_Base::SetStrands(), CPaintAlignment::UpdateFeatures(), wxT, and x_ExecuteCommand().

OnSubstitute()

void CAlignmentAssistant::OnSubstitute

(

wxCommandEvent &

event

)

Definition at line 691 of file alignment_assistant.cpp.

References CPaintAlignment::EnableSubstitute(), and m_Panel.

OnTarget()

void CAlignmentAssistant::OnTarget

(

wxCommandEvent &

event

)

Definition at line 1622 of file alignment_assistant.cpp.

References i, label, m_Labels, m_Panel, and CPaintAlignment::SetTarget().

Referenced by CreateControls().

OnValidate()

void CAlignmentAssistant::OnValidate

(

wxCommandEvent &

event

)

Definition at line 1677 of file alignment_assistant.cpp.

References CValidErrItem::ConvertSeverity(), CSeq_align_Handle::GetAnnot(), CSeq_entry_Handle::GetCompleteSeq_entry(), CObjectManager::GetInstance(), m_Alignment, m_TopSeqEntry, NULL, CGenericReportDlg::SetText(), ToWxString(), and wxT.

ReportPos()

void CAlignmentAssistant::ReportPos	(	int	pos,
		const string &	label
	)

Definition at line 518 of file alignment_assistant.cpp.

References _, NStr::IntToString(), label, and ToWxString().

Referenced by CPaintAlignment::OnPaint().

ReportRange()

void CAlignmentAssistant::ReportRange	(	int	pos1,
		int	pos2,
		const string &	label
	)

Definition at line 524 of file alignment_assistant.cpp.

References _, NStr::IntToString(), label, m_Range, and ToWxString().

Referenced by CPaintAlignment::OnPaint().

ReportUnresolvedBioseqs()

void CAlignmentAssistant::ReportUnresolvedBioseqs ( void  )

private

Definition at line 559 of file alignment_assistant.cpp.

References CSeq_align_Base::C_Segs::e_Denseg, CSeq_id::eContent, CScope::GetBioseqHandle(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CDense_seg_Base::GetNumseg(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CDense_seg::GetSeq_id(), CDense_seg_Base::IsSetDim(), CDense_seg_Base::IsSetIds(), CDense_seg_Base::IsSetLens(), CDense_seg_Base::IsSetNumseg(), CDense_seg_Base::IsSetStarts(), NStr::Join(), label, m_Alignment, CGenericReportDlg::SetText(), ToWxString(), CSeq_align_Base::C_Segs::Which(), and wxT.

Referenced by CAlignmentAssistant().

ShowToolTips()

bool CAlignmentAssistant::ShowToolTips ( )

static

Should we show tooltips?

Should we show tooltips?

Definition at line 484 of file alignment_assistant.cpp.

TranslateLocations()

void CAlignmentAssistant::TranslateLocations	(	CRef< CSeq_loc >	loc,
		vector< pair< CRef< CSeq_loc >, CBioseq_Handle > > &	locations
	)

Definition at line 1546 of file alignment_assistant.cpp.

References CPaintAlignment::AlignPosToSeqPos(), CSeq_loc::Assign(), CSerialObject::Assign(), CSeq_loc_I::Delete(), CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, eExtreme_Positional, CScope::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CSeq_align_Base::C_Segs::GetDenseg(), CDense_seg_Base::GetDim(), CSeq_loc_CI::GetFuzzFrom(), CSeq_loc_CI::GetFuzzTo(), CSeq_loc_CI::GetRange(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_align_Handle::GetScope(), CSeq_align_Handle::GetSegs(), CSeq_align_Handle::GetSeq_align(), CDense_seg::GetSeq_id(), CSeq_align::GetSeqStrand(), CSeq_loc::GetStart(), CSeq_loc_CI::GetStrand(), CSeq_loc_CI::IsEmpty(), IsReverse(), m_Alignment, m_Panel, CSeq_loc_I::MakeSeq_loc(), CInt_fuzz::Negative(), compile_time_bits::range(), CRef< C, Locker >::Reset(), CSeq_loc_I::ResetFuzzFrom(), CSeq_loc_I::ResetFuzzTo(), Reverse(), CSeq_loc_I::SetFrom(), CSeq_loc_I::SetFuzzFrom(), CSeq_loc_I::SetFuzzTo(), CSeq_loc::SetId(), CSeq_loc_I::SetStrand(), CSeq_loc_I::SetTo(), swap(), and CSeq_loc_Base::Which().

Referenced by CAlignCDSAddPanel::GetCommand(), CAlignRNAAddPanel::GetCommand(), and CAlignOtherAddPanel::GetCommand().

TrimQualityScores()

void CAlignmentAssistant::TrimQualityScores ( CBioseq_Handle  bsh, int  from, int  to, CRef< CCmdComposite >  command  )

private

Definition at line 1307 of file alignment_assistant.cpp.

References AdjustLoc(), CSerialObject::Assign(), command, CSeq_graph_Base::C_Graph::e_Byte, CSeq_annot_Base::C_Data::e_Graph, CSeq_graph_Base::C_Graph::e_Int, CSeq_graph_Base::C_Graph::e_Real, CSeq_loc_CI::eEmpty_Skip, CSeq_loc_CI::eOrder_Positional, CSeq_graph_Base::C_Graph::GetByte(), CSeq_graph_Base::GetComp(), CRange_Base::GetFrom(), CSeq_graph_Base::GetGraph(), CSeq_graph_Base::C_Graph::GetInt(), CSeq_graph_Base::GetLoc(), CMappedGraph::GetOriginalGraph(), CBioseq_Handle::GetRangeSeq_loc(), CSeq_graph_Base::C_Graph::GetReal(), CMappedGraph::GetSeq_graph_Handle(), CRange_Base::GetTo(), CByte_graph_Base::GetValues(), CInt_graph_Base::GetValues(), CReal_graph_Base::GetValues(), CSeq_graph_Base::IsSetComp(), CSeq_graph_Base::IsSetLoc(), CSeq_graph_Base::ResetLoc(), CByte_graph_Base::ResetValues(), CInt_graph_Base::ResetValues(), CReal_graph_Base::ResetValues(), CSeq_graph_Base::C_Graph::SetByte(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::C_Graph::SetInt(), CSeq_graph_Base::SetLoc(), CSeq_graph_Base::SetNumval(), CSeq_graph_Base::C_Graph::SetReal(), CByte_graph_Base::SetValues(), CInt_graph_Base::SetValues(), CReal_graph_Base::SetValues(), and CSeq_graph_Base::C_Graph::Which().

Referenced by DeleteSelection().

x_ExecuteCommand()

bool CAlignmentAssistant::x_ExecuteCommand ( IEditCommand *  command )

private

Definition at line 666 of file alignment_assistant.cpp.

References command, ICommandProccessor::Execute(), m_CmdProcessor, and m_TopSeqEntry.

Referenced by CreateFeature(), DeleteSelection(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), OnPropagateFeatures(), OnRemoveSeqFromAlign(), and OnReverseStrand().

Member Data Documentation

m_Alignment

CSeq_align_Handle CAlignmentAssistant::m_Alignment

private

Definition at line 166 of file alignment_assistant.hpp.

Referenced by AdjustAlign(), CreateControls(), CreateFeature(), DeleteSelection(), GetAlignment(), GetFeatures(), OnPropagateFeatures(), OnRemoveSeqFromAlign(), OnReverseStrand(), OnValidate(), ReportUnresolvedBioseqs(), and TranslateLocations().

m_CmdProcessor

ICommandProccessor* CAlignmentAssistant::m_CmdProcessor

private

Definition at line 167 of file alignment_assistant.hpp.

Referenced by x_ExecuteCommand().

m_FeatRanges

vector<vector<vector<pair<TSeqPos,TSeqPos> > > > CAlignmentAssistant::m_FeatRanges

private

Definition at line 170 of file alignment_assistant.hpp.

Referenced by CreateControls(), CreateFeature(), DeleteSelection(), GetFeatures(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), OnPropagateFeatures(), OnRemoveSeqFromAlign(), and OnReverseStrand().

m_FeatStrand

vector<vector<CBioseq_Handle::EVectorStrand> > CAlignmentAssistant::m_FeatStrand

private

Definition at line 172 of file alignment_assistant.hpp.

Referenced by CreateControls(), CreateFeature(), DeleteSelection(), GetFeatures(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), OnPropagateFeatures(), OnRemoveSeqFromAlign(), and OnReverseStrand().

m_FeatTypes

vector<vector<pair<string,CSeqFeatData::ESubtype> > > CAlignmentAssistant::m_FeatTypes

private

Definition at line 171 of file alignment_assistant.hpp.

Referenced by CreateControls(), CreateFeature(), DeleteSelection(), GetFeatures(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), OnPropagateFeatures(), OnRemoveSeqFromAlign(), and OnReverseStrand().

m_GoTo_TextCtrl

wxTextCtrl* CAlignmentAssistant::m_GoTo_TextCtrl

private

Definition at line 175 of file alignment_assistant.hpp.

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

m_GoToSeq_TextCtrl

wxTextCtrl* CAlignmentAssistant::m_GoToSeq_TextCtrl

private

Definition at line 176 of file alignment_assistant.hpp.

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

m_is_nucleotide

bool CAlignmentAssistant::m_is_nucleotide

private

Definition at line 177 of file alignment_assistant.hpp.

Referenced by GetFeatures(), IsNucleotide(), and IsSelectionAndClean().

m_Labels

vector<string> CAlignmentAssistant::m_Labels

private

Definition at line 178 of file alignment_assistant.hpp.

Referenced by CreateControls(), GetFeatures(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), OnRemoveSeqFromAlign(), and OnTarget().

m_Panel

CPaintAlignment* CAlignmentAssistant::m_Panel

private

Definition at line 168 of file alignment_assistant.hpp.

Referenced by CreateControls(), CreateFeature(), DeleteSelection(), Init(), IsSelectionAndClean(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), OnExportCont(), OnExportInter(), OnFeatures(), OnGoTo(), OnGoToSeq(), OnPropagateFeatures(), OnRemoveSeqFromAlign(), OnReverseStrand(), OnSubstitute(), OnTarget(), and TranslateLocations().

m_Range

wxStaticText* CAlignmentAssistant::m_Range

private

Definition at line 174 of file alignment_assistant.hpp.

Referenced by CreateControls(), and ReportRange().

m_target_submenu

wxMenu* CAlignmentAssistant::m_target_submenu

private

Definition at line 179 of file alignment_assistant.hpp.

Referenced by CreateControls(), and OnRemoveSeqFromAlign().

m_TopSeqEntry

CSeq_entry_Handle CAlignmentAssistant::m_TopSeqEntry

private

Definition at line 165 of file alignment_assistant.hpp.

Referenced by CreateFeature(), DeleteSelection(), GetAlignment(), IsNucleotide(), IsSelectionAndClean(), OnAddAlignCDS(), OnAddAlignOther(), OnAddAlignRNA(), OnValidate(), and x_ExecuteCommand().

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

• include/gui/widgets/edit/alignment_assistant.hpp
• src/gui/widgets/edit/alignment_assistant.cpp