Search Toolkit Book for CPaintSequence

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

Inheritance diagram for CPaintSequence:

Collaboration diagram for CPaintSequence:

Public Member Functions
	CPaintSequence ()

	CPaintSequence (wxWindow *parent, const string &seq, const vector< int > &seq_len, const vector< vector< pair< TSeqPos, TSeqPos > > > &feat_ranges, const vector< pair< string, objects::CSeqFeatData::ESubtype > > &feat_types, const vector< objects::CBioseq_Handle::EVectorStrand > &feat_strand, const vector< int > &feat_frames, const vector< CRef< objects::CGenetic_code > > &genetic_code, const vector< bool > &feat_partial5, const string &allowed_char_set, const vector< string > &real_prot, const vector< bool > &read_only, const unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > > &prot_feat_ranges, const int start=0, wxWindowID id=wxID_ANY, const wxPoint &pos=wxDefaultPosition, const wxSize &size=wxDefaultSize)

virtual	~CPaintSequence ()

void	InitPanel ()

void	OnMouseClick (wxMouseEvent &evt)

void	OnKeyDown (wxKeyEvent &event)

void	OnChar (wxKeyEvent &event)

void	OnMouseDrag (wxMouseEvent &evt)

void	OnMouseDown (wxMouseEvent &evt)

void	OnCopy (wxCommandEvent &event)

void	OnCut (wxCommandEvent &event)

void	OnPaste (wxCommandEvent &event)

string	GetSeq ()

int	GetLength ()

void	SetPos (int pos)

void	SetRange (int pos1, int pos2)

void	Search (const string &val)

vector< int > &	GetSeqLen ()

vector< bool > &	GetReadOnly ()

void	UpdateData ()

void	EnableTranslation (bool enable)

void	EnableTranslation1 (bool enable)

void	EnableTranslation2 (bool enable)

void	EnableRevTranslation (bool enable)

void	EnableRevTranslation1 (bool enable)

void	EnableRevTranslation2 (bool enable)

void	EnableComplement (bool enable)

void	EnableFeatures (bool enable)

void	EnableOnTheFly (bool enable)

void	EnableMismatch (bool enable)

bool	IsClipboard ()

bool	IsSelection ()

pair< int, int >	GetSelection ()

virtual void	OnPaint (wxPaintEvent &event)
	Painting. More...

virtual void	OnEraseBackground (wxEraseEvent &event)

virtual wxCoord	OnGetRowHeight (size_t row) const

virtual void	OnUpdate ()
	Notification for the derived class that moment is good for doing its update and drawing stuff. More...

void	OnResize (wxSizeEvent &)

void	UpdateFeatures (const vector< vector< pair< TSeqPos, TSeqPos > > > &feat_ranges, const vector< pair< string, objects::CSeqFeatData::ESubtype > > &feat_types, const vector< objects::CBioseq_Handle::EVectorStrand > &feat_strand, const vector< int > &feat_frames, const vector< CRef< objects::CGenetic_code > > &genetic_code, const vector< bool > &feat_partial5, const vector< string > &real_prot, const unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > > &prot_feat_ranges)

void	SetClean (bool clean)

bool	GetClean ()

string *	GetFindString (bool is_nuc, bool is_revcomp, const string &choice)

set< int > &	SetHighlights ()

TSeqPos	GetFeatureStart (int i, int j)

TSeqPos	GetFeatureStop (int i, int j)

TSeqPos	GetProtFeatureStart (int i, int k, int j)

TSeqPos	GetProtFeatureStop (int i, int k, int j)

Private Member Functions
void	NormalizeCursorColRows ()

void	InsertChar (int uc)

void	DeleteChar ()

void	ScrollWithCursor ()

void	SeqPosToColRow ()

void	ColRowToSeqPos ()

unsigned int	PosToSegment ()

void	ClearScreen (wxGraphicsContext *gc)

void	CalculateFontWidthAndHeight (wxGraphicsContext *gc)

int	CalculateNumCols ()

void	DrawTextLine (const string &substr, int &y_label, int row, wxGraphicsContext *gc, size_t &seq_pos)

void	DrawTextCell (const wxString &substr, int col, int row, unsigned int seq_pos, int x, int &y, const vector< unsigned int > &feats_in_row, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

void	DrawCursor (int col, int row, int x, int &y, wxGraphicsContext *gc) const

void	DrawTranslation (int x, int &y, unsigned int seq_pos, wxGraphicsContext *gc) const

void	DrawOffsetTranslation (int x, int y, unsigned int seq_pos, int offset, const string &prot, wxGraphicsContext *gc) const

void	DrawComplement (int x, int &y, unsigned int seq_pos, wxGraphicsContext *gc) const

const wxPen *	GetColorForFeature (objects::CSeqFeatData::ESubtype subtype) const

void	DrawFeatures (int row, unsigned int seq_pos, int x, int &y, int y_base, const vector< unsigned int > &feats_in_row, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

void	DrawFeatureLabels (int row, int x, int &y, const vector< unsigned int > &feats_in_row, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

int	LeftMarginWidth ()

void	DrawLineNumber (unsigned int seq_pos, int x, int &y, wxGraphicsContext *gc) const

void	DrawOnTheFly (int x, int &y, int y_base, unsigned int seq_pos, int i, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

char	TranslateOnTheFly (unsigned int seq_pos, int i, const vector< unsigned int > &ranges, const vector< string > &translation, bool &left, bool &right) const

void	DrawMismatch (int x, int &y, int y_base, unsigned int seq_pos, int i, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

bool	MouseToSeqPos (wxPoint p, int &row, int &y_row)

void	DrawTripletMismatch (int x, int y, int y_base, int i, wxGraphicsContext *gc) const

void	DrawComplementLabel (int row, int x, int &y, wxGraphicsContext *gc) const

void	DrawOnTheFlyLabel (int x, int &y, bool is_exon_present, wxGraphicsContext *gc) const

void	DrawTranslationLabels (int row, int x, int &y, wxGraphicsContext *gc) const

void	DrawMismatchLabel (int x, int &y, bool is_exon_present, wxGraphicsContext *gc) const

void	TranslateCDS ()

void	MouseToFeature (wxPoint p, int row, int y0)

void	AdjustFeatureRange (int origin, int offset)

void	AdjustProtFeatRange (int origin, int offset, int i)

void	AdjustFeatStartStop (int origin, int offset, int &start, int &stop)

int	FindRowByCoord (int y, int &y_row)

int	TopMarginHeight ()

void	DrawLabelCell (unsigned int pos, int x, int &y, int row, const vector< unsigned int > &feats_in_row, const map< unsigned int, vector< unsigned int > > &feats_with_exons, wxGraphicsContext *gc) const

vector< unsigned int >	GetFeaturesInRow (int row) const

void	GetFeatWholeRange ()

vector< unsigned int >	IsExonPresent (int i, int row) const

map< unsigned int, vector< unsigned int > >	GetFeatsWithExons (int row, const vector< unsigned int > &feats_in_row) const

void	RefreshWithScroll ()

string	CutSelection ()

void	SetStartPos (void)

Private Attributes
string	m_Seq

string	m_Prot

string	m_Prot1

string	m_Prot2

string	m_Complement

string	m_RevProt

string	m_RevProt1

string	m_RevProt2

vector< int >	m_SeqLen

vector< vector< pair< TSeqPos, TSeqPos > > >	m_FeatRanges

unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > >	m_ProtFeatRanges

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

vector< int >	m_FeatFrames

vector< CRef< objects::CGenetic_code > >	m_GeneticCode

vector< bool >	m_Feat5Partial

vector< pair< TSeqPos, TSeqPos > >	m_FeatWholeRange

vector< vector< TSeqPos > >	m_FeatLengthBefore

vector< TSeqPos >	m_FeatTotalLength

vector< string >	m_Translated

vector< objects::CBioseq_Handle::EVectorStrand >	m_FeatStrand

wxFont	m_Font

int	m_FontHeight

int	m_FontWidth

int	m_NumRows

int	m_NumCols

int	m_CursorCol

int	m_CursorRow

int	m_LastRowLength

int	m_CursorSeq

bool	m_EnableTranslation

bool	m_EnableTranslation1

bool	m_EnableTranslation2

bool	m_EnableComplement

bool	m_EnableFeatures

bool	m_ContinueFeatures

bool	m_EnableOnTheFly

bool	m_EnableMismatch

bool	m_EnableRevTranslation

bool	m_EnableRevTranslation1

bool	m_EnableRevTranslation2

string	m_AllowedCharSet

vector< string >	m_RealProt

int	m_ShowTriplet

int	m_DragMin

int	m_DragMax

CEditSequence *	m_Parent

int	m_ShowTripletMismatch

int	m_ShowTripletTranslation

bool	m_Clean

set< int >	m_highlights

pair< int, int >	m_FeatureStart

pair< int, int >	m_FeatureStop

vector< bool >	m_read_only

int	m_start

bool	m_Down

Detailed Description

Definition at line 62 of file paint_sequence.hpp.

Constructor & Destructor Documentation

◆ CPaintSequence() [1/2]

CPaintSequence::CPaintSequence ( )

inline

Definition at line 67 of file paint_sequence.hpp.

◆ CPaintSequence() [2/2]

CPaintSequence::CPaintSequence	(	wxWindow *	parent,
		const string &	seq,
		const vector< int > &	seq_len,
		const vector< vector< pair< TSeqPos, TSeqPos > > > &	feat_ranges,
		const vector< pair< string, objects::CSeqFeatData::ESubtype > > &	feat_types,
		const vector< objects::CBioseq_Handle::EVectorStrand > &	feat_strand,
		const vector< int > &	feat_frames,
		const vector< CRef< objects::CGenetic_code > > &	genetic_code,
		const vector< bool > &	feat_partial5,
		const string &	allowed_char_set,
		const vector< string > &	real_prot,
		const vector< bool > &	read_only,
		const unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > > &	prot_feat_ranges,
		const int	start = `0`,
		wxWindowID	id = `wxID_ANY`,
		const wxPoint &	pos = `wxDefaultPosition`,
		const wxSize &	size = `wxDefaultSize`
	)

◆ ~CPaintSequence()

CPaintSequence::~CPaintSequence ( )

virtual

Definition at line 144 of file paint_sequence.cpp.

Member Function Documentation

◆ AdjustFeatStartStop()

void CPaintSequence::AdjustFeatStartStop	(	int	origin,
		int	offset,
		int &	start,
		int &	stop
	)

private

Definition at line 1868 of file paint_sequence.cpp.

References m_Seq, max(), offset, and origin.

Referenced by AdjustFeatureRange(), and AdjustProtFeatRange().

◆ AdjustFeatureRange()

void CPaintSequence::AdjustFeatureRange	(	int	origin,
		int	offset
	)

private

Definition at line 1833 of file paint_sequence.cpp.

References AdjustFeatStartStop(), AdjustProtFeatRange(), GetFeatWholeRange(), i, m_FeatRanges, offset, origin, and TranslateCDS().

Referenced by CutSelection(), DeleteChar(), InsertChar(), and OnPaste().

◆ AdjustProtFeatRange()

void CPaintSequence::AdjustProtFeatRange	(	int	origin,
		int	offset,
		int	i
	)

private

Definition at line 1851 of file paint_sequence.cpp.

References AdjustFeatStartStop(), i, m_ProtFeatRanges, offset, and origin.

Referenced by AdjustFeatureRange().

◆ CalculateFontWidthAndHeight()

void CPaintSequence::CalculateFontWidthAndHeight ( wxGraphicsContext * gc )

private

Definition at line 1000 of file paint_sequence.cpp.

References m_FontHeight, m_FontWidth, and m_Seq.

Referenced by InitPanel().

◆ CalculateNumCols()

int CPaintSequence::CalculateNumCols ( )

private

Definition at line 1022 of file paint_sequence.cpp.

References chars_per_group, int, LeftMarginWidth(), m_FontWidth, and space_between_groups.

Referenced by InitPanel(), OnPaint(), and SetStartPos().

◆ ClearScreen()

void CPaintSequence::ClearScreen ( wxGraphicsContext * gc )

private

Definition at line 988 of file paint_sequence.cpp.

Referenced by OnPaint().

◆ ColRowToSeqPos()

void CPaintSequence::ColRowToSeqPos ( )

private

Definition at line 815 of file paint_sequence.cpp.

References m_CursorCol, m_CursorRow, m_CursorSeq, and m_NumCols.

Referenced by InsertChar(), MouseToSeqPos(), and OnPaint().

◆ CutSelection()

string CPaintSequence::CutSelection ( )

private

Definition at line 1574 of file paint_sequence.cpp.

References _, AdjustFeatureRange(), i, m_CursorSeq, m_DragMax, m_DragMin, m_Parent, m_read_only, m_Seq, m_SeqLen, PosToSegment(), result, ScrollWithCursor(), SeqPosToColRow(), SetClean(), CEditSequence::ShowReadOnlyWarning(), swap(), and UpdateData().

Referenced by DeleteChar(), and OnCut().

◆ DeleteChar()

void CPaintSequence::DeleteChar ( )

private

Definition at line 369 of file paint_sequence.cpp.

References _, AdjustFeatureRange(), CutSelection(), m_CursorSeq, m_Parent, m_read_only, m_Seq, m_SeqLen, PosToSegment(), result, SetClean(), CEditSequence::ShowReadOnlyWarning(), and UpdateData().

Referenced by OnKeyDown().

◆ DrawComplement()

void CPaintSequence::DrawComplement	(	int	x,
		int &	y,
		unsigned int	seq_pos,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1336 of file paint_sequence.cpp.

References m_Complement, m_EnableComplement, and m_FontHeight.

Referenced by DrawTextCell().

◆ DrawComplementLabel()

void CPaintSequence::DrawComplementLabel	(	int	row,
		int	x,
		int &	y,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1415 of file paint_sequence.cpp.

References _, m_EnableComplement, and m_FontHeight.

Referenced by DrawLabelCell(), and OnMouseClick().

◆ DrawCursor()

void CPaintSequence::DrawCursor	(	int	col,
		int	row,
		int	x,
		int &	y,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1143 of file paint_sequence.cpp.

References m_CursorCol, m_CursorRow, m_FontWidth, and row.

Referenced by DrawTextCell().

◆ DrawFeatureLabels()

void CPaintSequence::DrawFeatureLabels	(	int	row,
		int	x,
		int &	y,
		const vector< unsigned int > &	feats_in_row,
		const map< unsigned int, vector< unsigned int > > &	feats_with_exons,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1371 of file paint_sequence.cpp.

References DrawMismatchLabel(), DrawOnTheFlyLabel(), CSeqFeatData::eSubtype_cdregion, i, label, m_EnableFeatures, m_FeatTypes, m_Font, and m_FontHeight.

Referenced by DrawLabelCell(), and MouseToFeature().

◆ DrawFeatures()

void CPaintSequence::DrawFeatures	(	int	row,
		unsigned int	seq_pos,
		int	x,
		int &	y,
		int	y_base,
		const vector< unsigned int > &	feats_in_row,
		const map< unsigned int, vector< unsigned int > > &	feats_with_exons,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1481 of file paint_sequence.cpp.

References DrawMismatch(), DrawOnTheFly(), f, first(), GetColorForFeature(), i, m_ContinueFeatures, m_EnableFeatures, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_FeatWholeRange, m_FontHeight, m_FontWidth, and space_between_groups.

Referenced by DrawTextCell().

◆ DrawLabelCell()

void CPaintSequence::DrawLabelCell	(	unsigned int	pos,
		int	x,
		int &	y,
		int	row,
		const vector< unsigned int > &	feats_in_row,
		const map< unsigned int, vector< unsigned int > > &	feats_with_exons,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1066 of file paint_sequence.cpp.

References DrawComplementLabel(), DrawFeatureLabels(), DrawLineNumber(), DrawTranslationLabels(), m_FontHeight, and row.

Referenced by DrawTextLine(), MouseToFeature(), and OnGetRowHeight().

◆ DrawLineNumber()

void CPaintSequence::DrawLineNumber	(	unsigned int	seq_pos,
		int	x,
		int &	y,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1357 of file paint_sequence.cpp.

References label, m_Font, and m_FontHeight.

Referenced by DrawLabelCell().

◆ DrawMismatch()

void CPaintSequence::DrawMismatch	(	int	x,
		int &	y,
		int	y_base,
		unsigned int	seq_pos,
		int	i,
		const map< unsigned int, vector< unsigned int > > &	feats_with_exons,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1298 of file paint_sequence.cpp.

References DrawTripletMismatch(), CSeqFeatData::eSubtype_cdregion, f, i, m_EnableMismatch, m_FeatTypes, m_Font, m_FontHeight, m_FontWidth, m_RealProt, m_Translated, prot, and TranslateOnTheFly().

Referenced by DrawFeatures().

◆ DrawMismatchLabel()

void CPaintSequence::DrawMismatchLabel	(	int	x,
		int &	y,
		bool	is_exon_present,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1328 of file paint_sequence.cpp.

References m_EnableMismatch, and m_FontHeight.

Referenced by DrawFeatureLabels(), MouseToFeature(), and OnMouseClick().

◆ DrawOffsetTranslation()

void CPaintSequence::DrawOffsetTranslation	(	int	x,
		int	y,
		unsigned int	seq_pos,
		int	offset,
		const string &	prot,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1193 of file paint_sequence.cpp.

References offset, and prot.

Referenced by DrawTranslation().

◆ DrawOnTheFly()

void CPaintSequence::DrawOnTheFly	(	int	x,
		int &	y,
		int	y_base,
		unsigned int	seq_pos,
		int	i,
		const map< unsigned int, vector< unsigned int > > &	feats_with_exons,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1272 of file paint_sequence.cpp.

References DrawTripletMismatch(), CSeqFeatData::eSubtype_cdregion, f, i, m_EnableOnTheFly, m_FeatTypes, m_Font, m_FontHeight, m_FontWidth, m_Translated, prot, and TranslateOnTheFly().

Referenced by DrawFeatures().

◆ DrawOnTheFlyLabel()

void CPaintSequence::DrawOnTheFlyLabel	(	int	x,
		int &	y,
		bool	is_exon_present,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1427 of file paint_sequence.cpp.

References _, m_EnableOnTheFly, m_Font, and m_FontHeight.

Referenced by DrawFeatureLabels(), MouseToFeature(), and OnMouseClick().

◆ DrawTextCell()

void CPaintSequence::DrawTextCell	(	const wxString &	substr,
		int	col,
		int	row,
		unsigned int	seq_pos,
		int	x,
		int &	y,
		const vector< unsigned int > &	feats_in_row,
		const map< unsigned int, vector< unsigned int > > &	feats_with_exons,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1077 of file paint_sequence.cpp.

References chars_per_group, DrawComplement(), DrawCursor(), DrawFeatures(), DrawTranslation(), set< Key, Compare >::end(), set< Key, Compare >::find(), label, m_DragMax, m_DragMin, m_Font, m_FontHeight, m_FontWidth, m_highlights, m_Seq, m_ShowTripletTranslation, row, and swap().

Referenced by DrawTextLine().

◆ DrawTextLine()

void CPaintSequence::DrawTextLine	(	const string &	substr,
		int &	y_label,
		int	row,
		wxGraphicsContext *	gc,
		size_t &	seq_pos
	)

private

Definition at line 1036 of file paint_sequence.cpp.

References chars_per_group, DrawLabelCell(), DrawTextCell(), GetFeatsWithExons(), GetFeaturesInRow(), i, LeftMarginWidth(), m_ContinueFeatures, m_FontWidth, m_NumCols, row, and space_between_groups.

Referenced by OnPaint().

◆ DrawTranslation()

void CPaintSequence::DrawTranslation	(	int	x,
		int &	y,
		unsigned int	seq_pos,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1153 of file paint_sequence.cpp.

References DrawOffsetTranslation(), m_EnableRevTranslation, m_EnableRevTranslation1, m_EnableRevTranslation2, m_EnableTranslation, m_EnableTranslation1, m_EnableTranslation2, m_FontHeight, m_Prot, m_Prot1, m_Prot2, m_RevProt, m_RevProt1, m_RevProt2, m_Seq, and offset.

Referenced by DrawTextCell().

◆ DrawTranslationLabels()

void CPaintSequence::DrawTranslationLabels	(	int	row,
		int	x,
		int &	y,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1441 of file paint_sequence.cpp.

References _, m_EnableRevTranslation, m_EnableRevTranslation1, m_EnableRevTranslation2, m_EnableTranslation, m_EnableTranslation1, m_EnableTranslation2, and m_FontHeight.

Referenced by DrawLabelCell(), and OnMouseClick().

◆ DrawTripletMismatch()

void CPaintSequence::DrawTripletMismatch	(	int	x,
		int	y,
		int	y_base,
		int	i,
		wxGraphicsContext *	gc
	)		const

private

Definition at line 1262 of file paint_sequence.cpp.

References i, m_FontHeight, and m_ShowTripletMismatch.

Referenced by DrawMismatch(), and DrawOnTheFly().

◆ EnableComplement()

void CPaintSequence::EnableComplement ( bool enable )

Definition at line 227 of file paint_sequence.cpp.

References m_EnableComplement, and RefreshWithScroll().

Referenced by CEditSequence::OnComplement().

◆ EnableFeatures()

void CPaintSequence::EnableFeatures ( bool enable )

Definition at line 233 of file paint_sequence.cpp.

References m_EnableFeatures, and RefreshWithScroll().

Referenced by CEditSequence::CreateControls(), and CEditSequence::OnFeatures().

◆ EnableMismatch()

void CPaintSequence::EnableMismatch ( bool enable )

Definition at line 247 of file paint_sequence.cpp.

References m_EnableMismatch, m_ShowTripletMismatch, and RefreshWithScroll().

Referenced by CEditSequence::CreateControls(), and CEditSequence::OnMismatch().

◆ EnableOnTheFly()

void CPaintSequence::EnableOnTheFly ( bool enable )

Definition at line 239 of file paint_sequence.cpp.

References m_EnableOnTheFly, m_ShowTripletMismatch, and RefreshWithScroll().

Referenced by CEditSequence::OnOnTheFly().

◆ EnableRevTranslation()

void CPaintSequence::EnableRevTranslation ( bool enable )

Definition at line 202 of file paint_sequence.cpp.

References m_EnableRevTranslation, m_ShowTripletTranslation, and RefreshWithScroll().

Referenced by CEditSequence::OnRevTranslate(), CEditSequence::OnRevTranslateAll(), CEditSequence::OnTranslateEverything(), and CEditSequence::OnTranslateNone().

◆ EnableRevTranslation1()

void CPaintSequence::EnableRevTranslation1 ( bool enable )

Definition at line 210 of file paint_sequence.cpp.

References m_EnableRevTranslation1, m_ShowTripletTranslation, and RefreshWithScroll().

Referenced by CEditSequence::OnRevTranslate1(), CEditSequence::OnRevTranslateAll(), CEditSequence::OnTranslateEverything(), and CEditSequence::OnTranslateNone().

◆ EnableRevTranslation2()

void CPaintSequence::EnableRevTranslation2 ( bool enable )

Definition at line 218 of file paint_sequence.cpp.

References m_EnableRevTranslation2, m_ShowTripletTranslation, and RefreshWithScroll().

Referenced by CEditSequence::OnRevTranslate2(), CEditSequence::OnRevTranslateAll(), CEditSequence::OnTranslateEverything(), and CEditSequence::OnTranslateNone().

◆ EnableTranslation()

void CPaintSequence::EnableTranslation ( bool enable )

Definition at line 178 of file paint_sequence.cpp.

References m_EnableTranslation, m_ShowTripletTranslation, and RefreshWithScroll().

Referenced by CEditSequence::OnTranslate(), CEditSequence::OnTranslateAll(), CEditSequence::OnTranslateEverything(), and CEditSequence::OnTranslateNone().

◆ EnableTranslation1()

void CPaintSequence::EnableTranslation1 ( bool enable )

Definition at line 186 of file paint_sequence.cpp.

References m_EnableTranslation1, m_ShowTripletTranslation, and RefreshWithScroll().

Referenced by CEditSequence::OnTranslate1(), CEditSequence::OnTranslateAll(), CEditSequence::OnTranslateEverything(), and CEditSequence::OnTranslateNone().

◆ EnableTranslation2()

void CPaintSequence::EnableTranslation2 ( bool enable )

Definition at line 194 of file paint_sequence.cpp.

References m_EnableTranslation2, m_ShowTripletTranslation, and RefreshWithScroll().

Referenced by CEditSequence::OnTranslate2(), CEditSequence::OnTranslateAll(), CEditSequence::OnTranslateEverything(), and CEditSequence::OnTranslateNone().

◆ FindRowByCoord()

int CPaintSequence::FindRowByCoord	(	int	y,
		int &	y_row
	)

private

Definition at line 496 of file paint_sequence.cpp.

References OnGetRowHeight(), row, and TopMarginHeight().

Referenced by MouseToSeqPos().

◆ GetClean()

bool CPaintSequence::GetClean ( )

Definition at line 340 of file paint_sequence.cpp.

References m_Clean.

Referenced by CEditSequence::IsSelectionAndClean(), and CEditSequence::OnClose().

◆ GetColorForFeature()

const wxPen * CPaintSequence::GetColorForFeature ( objects::CSeqFeatData::ESubtype subtype ) const

private

Definition at line 1346 of file paint_sequence.cpp.

References CSeqFeatData::eSubtype_cdregion.

Referenced by DrawFeatures().

◆ GetFeatsWithExons()

map< unsigned int, vector< unsigned int > > CPaintSequence::GetFeatsWithExons	(	int	row,
		const vector< unsigned int > &	feats_in_row
	)		const

private

Definition at line 1977 of file paint_sequence.cpp.

References i, IsExonPresent(), and row.

Referenced by DrawTextLine(), MouseToFeature(), OnGetRowHeight(), and OnMouseClick().

◆ GetFeaturesInRow()

vector< unsigned int > CPaintSequence::GetFeaturesInRow ( int row ) const

private

Definition at line 1394 of file paint_sequence.cpp.

References i, m_FeatWholeRange, m_NumCols, and row.

Referenced by DrawTextLine(), MouseToFeature(), OnGetRowHeight(), and OnMouseClick().

◆ GetFeatureStart()

TSeqPos CPaintSequence::GetFeatureStart	(	int	i,
		int	j
	)

Definition at line 1819 of file paint_sequence.cpp.

References i, m_FeatRanges, and m_FeatStrand.

Referenced by CEditSequence::AdjustFeatureLocations().

◆ GetFeatureStop()

TSeqPos CPaintSequence::GetFeatureStop	(	int	i,
		int	j
	)

Definition at line 1826 of file paint_sequence.cpp.

References i, m_FeatRanges, and m_FeatStrand.

Referenced by CEditSequence::AdjustFeatureLocations().

◆ GetFeatWholeRange()

void CPaintSequence::GetFeatWholeRange ( )

private

Definition at line 1930 of file paint_sequence.cpp.

References first(), i, m_FeatLengthBefore, m_FeatRanges, m_FeatTotalLength, m_FeatWholeRange, and max().

Referenced by AdjustFeatureRange(), and UpdateFeatures().

◆ GetFindString()

string * CPaintSequence::GetFindString	(	bool	is_nuc,
		bool	is_revcomp,
		const string &	choice
	)

Definition at line 1745 of file paint_sequence.cpp.

References m_Complement, m_Prot, m_Prot1, m_Prot2, m_RevProt, m_RevProt1, m_RevProt2, m_Seq, NULL, and str().

Referenced by CFindEditSequence::FindMatchPositions().

◆ GetLength()

int CPaintSequence::GetLength ( void )

Definition at line 1773 of file paint_sequence.cpp.

References m_Seq.

Referenced by CFindEditSequence::FindMatchPositions(), and CEditSequence::OnRange().

◆ GetProtFeatureStart()

TSeqPos CPaintSequence::GetProtFeatureStart	(	int	i,
		int	k,
		int	j
	)

inline

Definition at line 123 of file paint_sequence.hpp.

References i, and m_ProtFeatRanges.

Referenced by CEditSequence::AdjustProtFeatureLocations().

◆ GetProtFeatureStop()

TSeqPos CPaintSequence::GetProtFeatureStop	(	int	i,
		int	k,
		int	j
	)

inline

Definition at line 124 of file paint_sequence.hpp.

References i, and m_ProtFeatRanges.

Referenced by CEditSequence::AdjustProtFeatureLocations().

◆ GetReadOnly()

vector<bool>& CPaintSequence::GetReadOnly ( )

inline

Definition at line 88 of file paint_sequence.hpp.

References m_read_only.

Referenced by CEditSequence::OnAccept().

◆ GetSelection()

pair< int, int > CPaintSequence::GetSelection ( void )

Definition at line 1736 of file paint_sequence.cpp.

References m_DragMax, m_DragMin, and swap().

Referenced by CEditSequence::CreateFeature(), and CEditSequence::CreateRegulatory().

◆ GetSeq()

string CPaintSequence::GetSeq ( void )

Definition at line 310 of file paint_sequence.cpp.

References m_Seq, and NStr::TruncateSpaces().

Referenced by CEditSequence::OnAccept().

◆ GetSeqLen()

vector< int > & CPaintSequence::GetSeqLen ( )

Definition at line 315 of file paint_sequence.cpp.

References m_SeqLen.

Referenced by CEditSequence::OnAccept().

◆ InitPanel()

void CPaintSequence::InitPanel ( )

Definition at line 122 of file paint_sequence.cpp.

References CalculateFontWidthAndHeight(), CalculateNumCols(), m_Font, m_NumCols, m_NumRows, and m_Seq.

Referenced by CEditSequence::CEditSequence().

◆ InsertChar()

void CPaintSequence::InsertChar ( int uc )

private

Definition at line 345 of file paint_sequence.cpp.

References AdjustFeatureRange(), ColRowToSeqPos(), m_CursorSeq, m_Parent, m_read_only, m_Seq, m_SeqLen, PosToSegment(), SeqPosToColRow(), SetClean(), CEditSequence::ShowReadOnlyWarning(), tolower(), and UpdateData().

Referenced by OnChar().

◆ IsClipboard()

bool CPaintSequence::IsClipboard ( )

Definition at line 1700 of file paint_sequence.cpp.

References data, i, m_AllowedCharSet, str(), and NStr::ToLower().

Referenced by CEditSequence::IsClipboard().

◆ IsExonPresent()

vector< unsigned int > CPaintSequence::IsExonPresent	(	int	i,
		int	row
	)		const

private

Definition at line 1957 of file paint_sequence.cpp.

References i, m_FeatRanges, m_NumCols, and row.

Referenced by GetFeatsWithExons().

◆ IsSelection()

bool CPaintSequence::IsSelection ( )

Definition at line 1728 of file paint_sequence.cpp.

References m_DragMax, and m_DragMin.

Referenced by CEditSequence::IsSelection(), and CEditSequence::IsSelectionAndClean().

◆ LeftMarginWidth()

int CPaintSequence::LeftMarginWidth ( )

private

Definition at line 491 of file paint_sequence.cpp.

References chars_per_group, and m_FontWidth.

Referenced by CalculateNumCols(), DrawTextLine(), and MouseToSeqPos().

◆ MouseToFeature()

void CPaintSequence::MouseToFeature	(	wxPoint	p,
		int	row,
		int	y0
	)

private

Definition at line 533 of file paint_sequence.cpp.

References DrawFeatureLabels(), DrawLabelCell(), DrawMismatchLabel(), DrawOnTheFlyLabel(), map_checker< Container >::end(), CSeqFeatData::eSubtype_cdregion, map_checker< Container >::find(), GetFeatsWithExons(), GetFeaturesInRow(), i, m_CursorSeq, m_EnableFeatures, m_FeatRanges, m_FeatTypes, m_FeatureStart, m_FeatureStop, m_FontHeight, max(), NULL, and row.

Referenced by OnMouseDown().

◆ MouseToSeqPos()

bool CPaintSequence::MouseToSeqPos	(	wxPoint	p,
		int &	row,
		int &	y_row
	)

private

Definition at line 514 of file paint_sequence.cpp.

References chars_per_group, ColRowToSeqPos(), FindRowByCoord(), LeftMarginWidth(), m_CursorCol, m_CursorRow, m_FontWidth, row, and space_between_groups.

Referenced by OnMouseClick(), OnMouseDown(), and OnMouseDrag().

◆ NormalizeCursorColRows()

void CPaintSequence::NormalizeCursorColRows ( )

private

Definition at line 477 of file paint_sequence.cpp.

References m_CursorCol, m_CursorRow, m_LastRowLength, m_NumCols, and m_NumRows.

Referenced by OnChar(), OnKeyDown(), OnMouseClick(), and RefreshWithScroll().

◆ OnChar()

void CPaintSequence::OnChar ( wxKeyEvent & event )

Definition at line 408 of file paint_sequence.cpp.

References InsertChar(), m_AllowedCharSet, NormalizeCursorColRows(), ScrollWithCursor(), and tolower().

◆ OnCopy()

void CPaintSequence::OnCopy ( wxCommandEvent & event )

Definition at line 1557 of file paint_sequence.cpp.

References m_DragMax, m_DragMin, m_Seq, and swap().

Referenced by CEditSequence::OnCopy().

◆ OnCut()

void CPaintSequence::OnCut ( wxCommandEvent & event )

Definition at line 1636 of file paint_sequence.cpp.

References CutSelection(), and result.

Referenced by CEditSequence::OnCut().

◆ OnEraseBackground()

void CPaintSequence::OnEraseBackground ( wxEraseEvent & event )

virtual

Definition at line 970 of file paint_sequence.cpp.

◆ OnGetRowHeight()

wxCoord CPaintSequence::OnGetRowHeight ( size_t row ) const

virtual

Definition at line 135 of file paint_sequence.cpp.

References DrawLabelCell(), GetFeatsWithExons(), GetFeaturesInRow(), NULL, r(), and row.

Referenced by FindRowByCoord().

◆ OnKeyDown()

void CPaintSequence::OnKeyDown ( wxKeyEvent & event )

Definition at line 421 of file paint_sequence.cpp.

References abs, DeleteChar(), m_CursorCol, m_CursorRow, m_CursorSeq, m_DragMax, m_DragMin, m_Seq, NormalizeCursorColRows(), ScrollWithCursor(), and SeqPosToColRow().

◆ OnMouseClick()

void CPaintSequence::OnMouseClick ( wxMouseEvent & evt )

◆ OnMouseDown()

void CPaintSequence::OnMouseDown ( wxMouseEvent & evt )

Definition at line 787 of file paint_sequence.cpp.

References m_Down, m_DragMax, m_DragMin, MouseToFeature(), MouseToSeqPos(), and row.

◆ OnMouseDrag()

void CPaintSequence::OnMouseDrag ( wxMouseEvent & evt )

Definition at line 743 of file paint_sequence.cpp.

References m_CursorSeq, m_Down, m_DragMax, m_DragMin, m_FeatRanges, m_FeatureStart, m_FeatureStop, m_FeatWholeRange, m_Seq, MouseToSeqPos(), row, and SetClean().

◆ OnPaint()

void CPaintSequence::OnPaint ( wxPaintEvent & event )

virtual

Painting.

Definition at line 882 of file paint_sequence.cpp.

References set< Key, Compare >::begin(), CalculateNumCols(), ClearScreen(), ColRowToSeqPos(), DrawTextLine(), set< Key, Compare >::end(), set< Key, Compare >::find(), m_CursorSeq, m_DragMax, m_DragMin, m_Font, m_highlights, m_LastRowLength, m_NumCols, m_NumRows, m_Seq, m_start, CEditSequence::ReportPos(), CEditSequence::ReportRange(), row, SeqPosToColRow(), SetStartPos(), swap(), and TopMarginHeight().

◆ OnPaste()

void CPaintSequence::OnPaste ( wxCommandEvent & event )

Definition at line 1654 of file paint_sequence.cpp.

References AdjustFeatureRange(), data, i, m_AllowedCharSet, m_CursorSeq, m_DragMax, m_DragMin, m_Parent, m_read_only, m_Seq, m_SeqLen, PosToSegment(), ScrollWithCursor(), SeqPosToColRow(), SetClean(), CEditSequence::ShowReadOnlyWarning(), str(), NStr::ToLower(), and UpdateData().

Referenced by CEditSequence::OnPaste().

◆ OnResize()

void CPaintSequence::OnResize ( wxSizeEvent & event )

Definition at line 983 of file paint_sequence.cpp.

◆ OnUpdate()

void CPaintSequence::OnUpdate ( )

virtual

Notification for the derived class that moment is good for doing its update and drawing stuff.

Definition at line 978 of file paint_sequence.cpp.

◆ PosToSegment()

unsigned int CPaintSequence::PosToSegment ( )

private

Definition at line 320 of file paint_sequence.cpp.

References i, m_CursorSeq, and m_SeqLen.

Referenced by CutSelection(), DeleteChar(), InsertChar(), and OnPaste().

◆ RefreshWithScroll()

void CPaintSequence::RefreshWithScroll ( )

private

Definition at line 170 of file paint_sequence.cpp.

References NormalizeCursorColRows(), ScrollWithCursor(), and SeqPosToColRow().

Referenced by EnableComplement(), EnableFeatures(), EnableMismatch(), EnableOnTheFly(), EnableRevTranslation(), EnableRevTranslation1(), EnableRevTranslation2(), EnableTranslation(), EnableTranslation1(), and EnableTranslation2().

◆ ScrollWithCursor()

void CPaintSequence::ScrollWithCursor ( )

private

Definition at line 402 of file paint_sequence.cpp.

References m_CursorRow.

Referenced by CutSelection(), OnChar(), OnKeyDown(), OnMouseClick(), OnPaste(), RefreshWithScroll(), Search(), SetPos(), SetRange(), and SetStartPos().

◆ Search()

void CPaintSequence::Search ( const string & val )

Definition at line 846 of file paint_sequence.cpp.

References NStr::FindNoCase(), m_CursorSeq, m_Seq, NPOS, ScrollWithCursor(), SeqPosToColRow(), and val.

Referenced by CEditSequence::OnGoTo().

◆ SeqPosToColRow()

void CPaintSequence::SeqPosToColRow ( )

private

Definition at line 807 of file paint_sequence.cpp.

References m_CursorCol, m_CursorRow, m_CursorSeq, and m_NumCols.

Referenced by CutSelection(), InsertChar(), OnKeyDown(), OnPaint(), OnPaste(), RefreshWithScroll(), Search(), SetPos(), SetRange(), and SetStartPos().

◆ SetClean()

void CPaintSequence::SetClean ( bool clean )

Definition at line 334 of file paint_sequence.cpp.

References CEditSequence::EnableCommit(), m_Clean, and m_Parent.

Referenced by CutSelection(), DeleteChar(), InsertChar(), CEditSequence::OnAccept(), OnMouseDrag(), and OnPaste().

◆ SetHighlights()

set< int > & CPaintSequence::SetHighlights ( void )

Definition at line 1778 of file paint_sequence.cpp.

References m_DragMax, m_DragMin, and m_highlights.

Referenced by CFindEditSequence::SetHighlights().

◆ SetPos()

void CPaintSequence::SetPos ( int pos )

Definition at line 820 of file paint_sequence.cpp.

References m_CursorSeq, m_Seq, ScrollWithCursor(), and SeqPosToColRow().

Referenced by CEditSequence::OnGoTo(), CFindEditSequence::OnNext(), and CFindEditSequence::OnPrev().

◆ SetRange()

void CPaintSequence::SetRange	(	int	pos1,
		int	pos2
	)

Definition at line 832 of file paint_sequence.cpp.

References m_CursorSeq, m_DragMax, m_DragMin, m_Seq, ScrollWithCursor(), and SeqPosToColRow().

Referenced by CEditSequence::OnRange().

◆ SetStartPos()

void CPaintSequence::SetStartPos ( void )

private

Definition at line 861 of file paint_sequence.cpp.

References CalculateNumCols(), m_CursorSeq, m_NumCols, m_start, CEditSequence::ReportPos(), ScrollWithCursor(), and SeqPosToColRow().

Referenced by OnPaint().

◆ TopMarginHeight()

int CPaintSequence::TopMarginHeight ( )

inlineprivate

Definition at line 162 of file paint_sequence.hpp.

Referenced by FindRowByCoord(), and OnPaint().

◆ TranslateCDS()

void CPaintSequence::TranslateCDS ( )

private

Definition at line 1786 of file paint_sequence.cpp.

References CSeqUtil::e_Iupacna, CSeqFeatData::eSubtype_cdregion, CSeqTranslator::fIs5PrimePartial, flags, CSeqTranslator::fRemoveTrailingX, i, m_Feat5Partial, m_FeatFrames, m_FeatRanges, m_FeatStrand, m_FeatTypes, m_GeneticCode, m_Seq, m_Translated, max(), NULL, CSeqManip::ReverseComplement(), swap(), NStr::ToLower(), and CSeqTranslator::Translate().

Referenced by AdjustFeatureRange(), OnMouseClick(), and UpdateFeatures().

◆ TranslateOnTheFly()

char CPaintSequence::TranslateOnTheFly	(	unsigned int	seq_pos,
		int	i,
		const vector< unsigned int > &	ranges,
		const vector< string > &	translation,
		bool &	left,
		bool &	right
	)		const

private

Definition at line 1205 of file paint_sequence.cpp.

References i, m_FeatFrames, m_FeatLengthBefore, m_FeatRanges, m_FeatStrand, m_FeatTotalLength, and prot.

Referenced by DrawMismatch(), and DrawOnTheFly().

◆ UpdateData()

void CPaintSequence::UpdateData ( )

Definition at line 255 of file paint_sequence.cpp.

References CSeqManip::Complement(), CSeqUtil::e_Iupacna, CSeqTranslator::fIs5PrimePartial, CSeqTranslator::fRemoveTrailingX, i, m_Complement, m_EnableComplement, m_EnableOnTheFly, m_EnableRevTranslation, m_EnableRevTranslation1, m_EnableRevTranslation2, m_EnableTranslation, m_EnableTranslation1, m_EnableTranslation2, m_FeatStrand, m_Prot, m_Prot1, m_Prot2, m_RevProt, m_RevProt1, m_RevProt2, m_Seq, minus(), plus(), CSeqManip::ReverseComplement(), NStr::ToLower(), and CSeqTranslator::Translate().

Referenced by CutSelection(), DeleteChar(), InsertChar(), CEditSequence::OnComplement(), CEditSequence::OnOnTheFly(), OnPaste(), CEditSequence::OnRevTranslate(), CEditSequence::OnRevTranslate1(), CEditSequence::OnRevTranslate2(), CEditSequence::OnRevTranslateAll(), CEditSequence::OnTranslate(), CEditSequence::OnTranslate1(), CEditSequence::OnTranslate2(), CEditSequence::OnTranslateAll(), CEditSequence::OnTranslateEverything(), and UpdateFeatures().

◆ UpdateFeatures()

void CPaintSequence::UpdateFeatures	(	const vector< vector< pair< TSeqPos, TSeqPos > > > &	feat_ranges,
		const vector< pair< string, objects::CSeqFeatData::ESubtype > > &	feat_types,
		const vector< objects::CBioseq_Handle::EVectorStrand > &	feat_strand,
		const vector< int > &	feat_frames,
		const vector< CRef< objects::CGenetic_code > > &	genetic_code,
		const vector< bool > &	feat_partial5,
		const vector< string > &	real_prot,
		const unordered_map< int, vector< vector< pair< TSeqPos, TSeqPos > > > > &	prot_feat_ranges
	)