Search Toolkit Book for CRawSeqToDeltaSeqByLoc

#include <gui/packages/pkg_sequence_edit/raw_seq_to_delta_by_loc.hpp>

Inheritance diagram for CRawSeqToDeltaSeqByLoc:

Collaboration diagram for CRawSeqToDeltaSeqByLoc:

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

	CRawSeqToDeltaSeqByLoc (wxWindow *parent, objects::CSeq_entry_Handle tse, wxWindowID id=10000, const wxString &caption=_("Convert Raw Sequence to Delta Sequence"), 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=10000, const wxString &caption=_("Convert Raw Sequence to Delta Sequence"), const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxSize(400, 300), long style=wxCAPTION\|wxRESIZE_BORDER\|wxSYSTEM_MENU\|wxCLOSE_BOX\|wxTAB_TRAVERSAL)
	Creation. More...

	~CRawSeqToDeltaSeqByLoc ()
	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	OnNewText (wxCommandEvent &event)

CRef< CCmdComposite >	apply (string title)

void	UseAlignCoords (objects::CBioseq_Handle bsh, vector< NRawToDeltaSeq::SGap > &gaps)

void	ComputeAlignCoords (objects::CBioseq_Handle bsh, int before, int after, int &real_before, int &real_after)

Public Member Functions inherited from CReportEditingDialog
virtual bool	Show (bool show=1)
	Report opening events in dialogs used in the editing package. More...

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

static void	UpdateDensegAlignment (const objects::CSeq_entry_Handle &tse, CRef< CCmdComposite > composite, const vector< NRawToDeltaSeq::SGap > &gaps, const bool use_align_coords)

static CRef< CCmdComposite >	ByAssemblyGapFeatures (objects::CSeq_entry_Handle seh)

Private Member Functions
CRef< CCmdComposite >	apply_impl (string title, map< objects::CObject_id::TId, objects::CObject_id::TId > &old_to_new, bool create_xref_map)

Static Private Member Functions
static void	x_UpdateRows (size_t num_rows, const vector< NRawToDeltaSeq::SGap > &gaps, const vector< TSignedSeqPos > &orig_starts, const vector< TSeqPos > &lens, const vector< objects::ENa_strand > &strands, const vector< CRef< objects::CScore > > &scores, vector< vector< vector< TSignedSeqPos > > > &all_new_starts, vector< vector< TSeqPos > > &all_new_lens, vector< vector< vector< objects::ENa_strand > > > &all_new_strands, vector< vector< CRef< objects::CScore > > > &all_new_scores, const bool use_align_coords, const objects::CSeq_align &align)

static CRef< objects::CSeq_align >	x_GetNewAlign (const size_t block, const objects::CSeq_align &align, const size_t num_rows, const vector< vector< vector< TSignedSeqPos > > > &all_new_starts, const vector< vector< TSeqPos > > &all_new_lens, const vector< vector< vector< objects::ENa_strand > > > &all_new_strands, const vector< vector< CRef< objects::CScore > > > &all_new_scores)

static CRef< CCmdComposite >	ByAssemblyGapFeatures_impl (objects::CSeq_entry_Handle seh, map< objects::CObject_id::TId, objects::CObject_id::TId > &old_to_new, bool create_xref_map)

Private Attributes
wxBoxSizer *	m_ScrollSizer

wxRadioButton *	m_CoordSeq

wxCheckBox *	m_AdjustCDS

wxTextCtrl *	m_LastStart

wxTextCtrl *	m_LastLength

objects::CSeq_entry_Handle	m_TopSeqEntry

Detailed Description

CRawSeqToDeltaSeqByLoc class declaration

Definition at line 102 of file raw_seq_to_delta_by_loc.hpp.

Constructor & Destructor Documentation

◆ CRawSeqToDeltaSeqByLoc() [1/2]

CRawSeqToDeltaSeqByLoc::CRawSeqToDeltaSeqByLoc ( )

Constructors.

Definition at line 117 of file raw_seq_to_delta_by_loc.cpp.

References Init().

◆ CRawSeqToDeltaSeqByLoc() [2/2]

CRawSeqToDeltaSeqByLoc::CRawSeqToDeltaSeqByLoc	(	wxWindow *	parent,
		objects::CSeq_entry_Handle	tse,
		wxWindowID	id = `10000`,
		const wxString &	caption = `_("Convert Raw Sequence to Delta Sequence")`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxCAPTION\|wxRESIZE_BORDER\|wxSYSTEM_MENU\|wxCLOSE_BOX\|wxTAB_TRAVERSAL`
	)

Definition at line 122 of file raw_seq_to_delta_by_loc.cpp.

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

◆ ~CRawSeqToDeltaSeqByLoc()

CRawSeqToDeltaSeqByLoc::~CRawSeqToDeltaSeqByLoc ( )

Destructor.

Definition at line 155 of file raw_seq_to_delta_by_loc.cpp.

Member Function Documentation

◆ apply()

CRef< CCmdComposite > CRawSeqToDeltaSeqByLoc::apply ( string title )

Definition at line 356 of file raw_seq_to_delta_by_loc.cpp.

References apply_impl().

Referenced by CSequenceEditingEventHandler::RawSeqToDeltaByLoc().

◆ apply_impl()

CRef< CCmdComposite > CRawSeqToDeltaSeqByLoc::apply_impl	(	string	title,
		map< objects::CObject_id::TId, objects::CObject_id::TId > &	old_to_new,
		bool	create_xref_map
	)

private

◆ ByAssemblyGapFeatures()

CRef< CCmdComposite > CRawSeqToDeltaSeqByLoc::ByAssemblyGapFeatures ( objects::CSeq_entry_Handle seh )

static

Definition at line 942 of file raw_seq_to_delta_by_loc.cpp.

References ByAssemblyGapFeatures_impl().

Referenced by CSequenceEditingEventHandler::RawSeqToDeltaByAssemblyGapFeatures().

◆ ByAssemblyGapFeatures_impl()

CRef< CCmdComposite > CRawSeqToDeltaSeqByLoc::ByAssemblyGapFeatures_impl	(	objects::CSeq_entry_Handle	seh,
		map< objects::CObject_id::TId, objects::CObject_id::TId > &	old_to_new,
		bool	create_xref_map
	)

staticprivate

◆ ComputeAlignCoords()

void CRawSeqToDeltaSeqByLoc::ComputeAlignCoords	(	objects::CBioseq_Handle	bsh,
		int	before,
		int	after,
		int &	real_before,
		int &	real_after
	)

Definition at line 520 of file raw_seq_to_delta_by_loc.cpp.

References CEditSeqEndsWithAlign::FindPosition(), CEditSeqEndsWithAlign::FindRow(), and row.

Referenced by UseAlignCoords().

◆ Create()

bool CRawSeqToDeltaSeqByLoc::Create	(	wxWindow *	parent,
		wxWindowID	id = `10000`,
		const wxString &	caption = `_("Convert Raw Sequence to Delta Sequence")`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxSize(400, 300)`,
		long	style = `wxCAPTION\|wxRESIZE_BORDER\|wxSYSTEM_MENU\|wxCLOSE_BOX\|wxTAB_TRAVERSAL`
	)

Creation.

Definition at line 134 of file raw_seq_to_delta_by_loc.cpp.

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

Referenced by CRawSeqToDeltaSeqByLoc().

◆ CreateControls()

void CRawSeqToDeltaSeqByLoc::CreateControls ( )

Creates the controls and sizers.

Definition at line 180 of file raw_seq_to_delta_by_loc.cpp.

References _, i, ID_CRAWTODELTA_CHECKBOX, ID_CRAWTODELTA_RADIOBUTTON, ID_CRAWTODELTA_RADIOBUTTON1, ID_CRAWTODELTA_SCROLLEDWINDOW, m_AdjustCDS, m_CoordSeq, m_LastLength, m_LastStart, m_ScrollSizer, m_TopSeqEntry, OnNewText(), and wxID_ANY.

Referenced by Create().

◆ GetBitmapResource()

wxBitmap CRawSeqToDeltaSeqByLoc::GetBitmapResource ( const wxString & name )

Retrieves bitmap resources.

Definition at line 334 of file raw_seq_to_delta_by_loc.cpp.

◆ GetIconResource()

wxIcon CRawSeqToDeltaSeqByLoc::GetIconResource ( const wxString & name )

Retrieves icon resources.

Definition at line 347 of file raw_seq_to_delta_by_loc.cpp.

◆ Init()

void CRawSeqToDeltaSeqByLoc::Init ( void )

Initialises member variables.

Definition at line 166 of file raw_seq_to_delta_by_loc.cpp.

References m_AdjustCDS, m_CoordSeq, m_ScrollSizer, and NULL.

Referenced by CRawSeqToDeltaSeqByLoc().

◆ OnNewText()

void CRawSeqToDeltaSeqByLoc::OnNewText ( wxCommandEvent & event )

Definition at line 282 of file raw_seq_to_delta_by_loc.cpp.

References _, m_LastLength, m_LastStart, m_ScrollSizer, and wxID_ANY.

Referenced by CreateControls().

◆ ShowToolTips()

bool CRawSeqToDeltaSeqByLoc::ShowToolTips ( )

static

Should we show tooltips?

Definition at line 325 of file raw_seq_to_delta_by_loc.cpp.

◆ UpdateDensegAlignment()

void CRawSeqToDeltaSeqByLoc::UpdateDensegAlignment	(	const objects::CSeq_entry_Handle &	tse,
		CRef< CCmdComposite >	composite,
		const vector< NRawToDeltaSeq::SGap > &	gaps,
		const bool	use_align_coords
	)

static

Definition at line 554 of file raw_seq_to_delta_by_loc.cpp.

References CCmdComposite::AddCommand(), cmd, CSeq_align_Handle::GetAnnot(), CSeq_annot_Handle::GetParentEntry(), x_GetNewAlign(), and x_UpdateRows().

Referenced by apply_impl(), and ByAssemblyGapFeatures_impl().

◆ UseAlignCoords()

void CRawSeqToDeltaSeqByLoc::UseAlignCoords	(	objects::CBioseq_Handle	bsh,
		vector< NRawToDeltaSeq::SGap > &	gaps
	)

Definition at line 503 of file raw_seq_to_delta_by_loc.cpp.

References ComputeAlignCoords(), and i.

Referenced by apply_impl().

◆ x_GetNewAlign()

CRef< CSeq_align > CRawSeqToDeltaSeqByLoc::x_GetNewAlign	(	const size_t	block,
		const objects::CSeq_align &	align,
		const size_t	num_rows,
		const vector< vector< vector< TSignedSeqPos > > > &	all_new_starts,
		const vector< vector< TSeqPos > > &	all_new_lens,
		const vector< vector< vector< objects::ENa_strand > > > &	all_new_strands,
		const vector< vector< CRef< objects::CScore > > > &	all_new_scores
	)

staticprivate

Definition at line 906 of file raw_seq_to_delta_by_loc.cpp.

References CSerialObject::Assign(), ctll::empty(), i, row, CSeq_align_Base::SetSegs(), and ncbi::grid::netcache::search::fields::size.

Referenced by UpdateDensegAlignment().

◆ x_UpdateRows()

void CRawSeqToDeltaSeqByLoc::x_UpdateRows	(	size_t	num_rows,
		const vector< NRawToDeltaSeq::SGap > &	gaps,
		const vector< TSignedSeqPos > &	orig_starts,
		const vector< TSeqPos > &	lens,
		const vector< objects::ENa_strand > &	strands,
		const vector< CRef< objects::CScore > > &	scores,
		vector< vector< vector< TSignedSeqPos > > > &	all_new_starts,
		vector< vector< TSeqPos > > &	all_new_lens,
		vector< vector< vector< objects::ENa_strand > > > &	all_new_strands,
		vector< vector< CRef< objects::CScore > > > &	all_new_scores,
		const bool	use_align_coords,
		const objects::CSeq_align &	align
	)