SeqBasic Class Reference

The parent class for all sequence types, including DNA, amino acids, features, restriction sites, ABI peaks, etc. More...

#include <SequenceCanvas.h>

Inheritance diagram for SeqBasic:

List of all members.


Public Member Functions
	SeqBasic (SequenceCanvas *ncan=NULL)
	Constructor.
virtual	~SeqBasic ()
	Destructor.
virtual void	init (SequenceCanvas *ncan=NULL)
	Initialization.
virtual void	initFromTVector (TVector *v)
	Set from a TVector class.
virtual int	arrange (int n)
virtual void	show (wxDC &dc)
	Arrange "chars" as line n.
virtual wxPoint	showText (int ystart, wxArrayString &tout)
	Show.
virtual wxString	whatsthis ()
	Returns the linetype.
virtual void	makeEndnumberLength ()
virtual bool	useDirectRoutines ()
	Do we draw directly (or do we use SeqPos)?
virtual int	getMarkSize ()
	Returns the length of the SeqPos marked part of the sequence.
virtual int	getRectSize ()
	Returns the number of SeqPos rectangles.
virtual wxRect	getRect (int i)
	Returns the SeqPos rect for a "char".
virtual int	getMark (int i)
	Returns the mark value for a "char".
virtual void	setMark (int i, int v)
	Sets the marking of a "char".
virtual int	getPos (int i)
	Returns the internal ID of the "char".
virtual void	setPos (int i, int v)
	Sets the internal ID of the "char".
virtual int	getLine (int y)
	Returns the line number for the y position.
virtual int	getItem (wxPoint pt, int line)
	Returns the "char" at that position.
virtual bool	isDisplayOnly ()
	Do we show something?
virtual void	logsize ()
	Some memory calculation for debugging, I think...
virtual void	editMode (bool on=true)
	Set edit mode for this sequence line.
virtual void	addHighlight (int from, int to, wxColour c)
	Adds a sequence highlight.
virtual wxColour	getHighlightColor (int pos, wxColour c)
	Sets the color to the highlight color, if the position is highlighted.
virtual void	clearHighlights ()
	Removes all highlights.
Public Attributes
wxString	s
	The sequence as a text; may be blank for some linetypes.
int	offset
int	endnumberlength
int	itemsperline
SequenceCanvas *	can
	The containing SequenceCanvas.
bool	takesMouseActions
bool	shown
Protected Member Functions
virtual int	arrange_direct (int n)
	Arrange quickly (bypassing SeqPos).
virtual void	show_direct (wxDC &dc)
Protected Attributes
wxArrayInt	highlight_begin
	Show quickly.
wxArrayInt	highlight_end
	Show quickly.
vector< wxColour >	highlight_color
SeqPos	pos
	Position class (empty when using direct routines).
int	force_add_line_number
	Default counter to add to the line number display; usually 0.

Detailed Description

The parent class for all sequence types, including DNA, amino acids, features, restriction sites, ABI peaks, etc.

Constructor & Destructor Documentation

SeqBasic::SeqBasic ( SequenceCanvas * ncan = NULL ) [inline]

Constructor.

SeqBasic::~SeqBasic ( ) [virtual]

Destructor.

Member Function Documentation

void SeqBasic::addHighlight ( int from,

int to,

wxColour c

) [virtual]

Adds a sequence highlight.

virtual int SeqBasic::arrange ( int n ) [inline, virtual]

Reimplemented in SeqNum, SeqDivider, SeqDNA, SeqAlign, SeqRestriction, SeqAA, SeqAAstructure, SeqABI, and SeqPlot.

virtual int SeqBasic::arrange_direct ( int n ) [inline, protected, virtual]

Arrange quickly (bypassing SeqPos).

Reimplemented in SeqDNA, SeqPrimer, SeqAA, SeqABI, SeqFeature, and SeqPlot.

void SeqBasic::clearHighlights ( ) [virtual]

Removes all highlights.

void SeqBasic::editMode ( bool on = true ) [virtual]

Set edit mode for this sequence line.

wxColour SeqBasic::getHighlightColor ( int pos,

wxColour c

) [virtual]

Sets the color to the highlight color, if the position is highlighted.

virtual int SeqBasic::getItem ( wxPoint pt,

int line

) [inline, virtual]

Returns the "char" at that position.

Reimplemented in SeqDNA, and SeqAA.

virtual int SeqBasic::getLine ( int y ) [inline, virtual]

Returns the line number for the y position.

Reimplemented in SeqDNA, and SeqAA.

virtual int SeqBasic::getMark ( int i ) [inline, virtual]

Returns the mark value for a "char".

Reimplemented in SeqDNA, and SeqAA.

virtual int SeqBasic::getMarkSize ( ) [inline, virtual]

Returns the length of the SeqPos marked part of the sequence.

Reimplemented in SeqDNA, and SeqAA.

virtual int SeqBasic::getPos ( int i ) [inline, virtual]

Returns the internal ID of the "char".

Reimplemented in SeqDNA, and SeqAA.

virtual wxRect SeqBasic::getRect ( int i ) [inline, virtual]

Returns the SeqPos rect for a "char".

Reimplemented in SeqDNA, and SeqAA.

virtual int SeqBasic::getRectSize ( ) [inline, virtual]

Returns the number of SeqPos rectangles.

Reimplemented in SeqDNA, and SeqAA.

void SeqBasic::init ( SequenceCanvas * ncan = NULL ) [virtual]

Initialization.

Reimplemented in SeqPlot.

virtual void SeqBasic::initFromTVector ( TVector * v ) [inline, virtual]

Set from a TVector class.

Reimplemented in SeqDivider, SeqDNA, SeqPrimer, SeqRestriction, SeqAA, SeqFeature, and SeqPlot.

virtual bool SeqBasic::isDisplayOnly ( ) [inline, virtual]

Do we show something?

Reimplemented in SeqNum, SeqDivider, SeqBlank, SeqRestriction, and SeqFeature.

void SeqBasic::logsize ( ) [virtual]

Some memory calculation for debugging, I think...

Reimplemented in SeqAA.

virtual void SeqBasic::makeEndnumberLength ( ) [inline, virtual]

Reimplemented in SeqDNA, and SeqAlign.

virtual void SeqBasic::setMark ( int i,

int v

) [inline, virtual]

Sets the marking of a "char".

Reimplemented in SeqDNA, and SeqAA.

virtual void SeqBasic::setPos ( int i,

int v

) [inline, virtual]

Sets the internal ID of the "char".

Reimplemented in SeqDNA, and SeqAA.

virtual void SeqBasic::show ( wxDC & dc ) [inline, virtual]

Arrange "chars" as line n.

Reimplemented in SeqNum, SeqDivider, SeqBlank, SeqDNA, SeqPrimer, SeqAlign, SeqRestriction, SeqAA, SeqAAstructure, SeqABI, SeqFeature, and SeqPlot.

virtual void SeqBasic::show_direct ( wxDC & dc ) [inline, protected, virtual]

Reimplemented in SeqDNA, SeqPrimer, SeqAA, SeqABI, SeqFeature, and SeqPlot.

virtual wxPoint SeqBasic::showText ( int ystart,

wxArrayString & tout

) [inline, virtual]

Show.

Reimplemented in SeqDNA, and SeqAA.

virtual bool SeqBasic::useDirectRoutines ( ) [inline, virtual]

Do we draw directly (or do we use SeqPos)?

Reimplemented in SeqDNA, SeqPrimer, SeqRestriction, SeqAA, SeqABI, SeqFeature, and SeqPlot.