SeqAA Class Reference

Sequence display class showing amino acids. More...

#include <SequenceCanvas.h>

Inheritance diagram for SeqAA:

List of all members.

Public Member Functions
	SeqAA (SequenceCanvas *ncan=NULL)
	Constructor.
virtual	~SeqAA ()
	Destructor.
virtual int	arrange (int n)
	Arrange "chars" as line n.
virtual void	show (wxDC &dc)
	Show.
virtual wxPoint	showText (int ystart, wxArrayString &tout)
	Show as text (rarely used).
virtual void	initFromTVector (TVector *v)
	Set from a TVector class.
virtual void	initFromString (wxString t)
	Set from a string.
virtual void	analyzeProteases ()
	Find protease cuts.
virtual void	updateProteases ()
	Set protease cuts in display.
virtual void	fixOffsets (TVector *v)
	Feature offsets fix (see SeqFeature).
virtual wxString	whatsthis ()
	Returns the linetype.
virtual int	arrange_direct (int n)
	Arrange quickly (bypassing SeqPos).
virtual void	show_direct (wxDC &dc)
	Show quickly.
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 void	logsize ()
	Some internal debugging thingy.
Public Attributes
TVector *	vec
	Pointer to the original sequence data.
int	mode
int	disp
bool	primaryMode
bool	showNumbers
char	unknownAA
wxArrayTProteaseCut	pc
	List of protease cuts.
wxString	pa_w
wxArrayTProtease	proteases
	List of proteases to look for.
wxArrayInt	offsets
wxArrayInt	pa_wa
wxArrayTVectorItem	offset_items

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Detailed Description

Sequence display class showing amino acids.

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Constructor & Destructor Documentation

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

Constructor.

SeqAA::~SeqAA (   )  [virtual]

Destructor.

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Member Function Documentation

void SeqAA::analyzeProteases (   )  [virtual]

Find protease cuts.

int SeqAA::arrange (  int  n  )  [virtual]

Arrange "chars" as line n. Reimplemented from SeqBasic.

int SeqAA::arrange_direct (  int  n  )  [virtual]

Arrange quickly (bypassing SeqPos). Reimplemented from SeqBasic.

void SeqAA::fixOffsets (  TVector *  v  )  [virtual]

Feature offsets fix (see SeqFeature).

int SeqAA::getItem (  wxPoint  pt, int  line )  [virtual]

Returns the "char" at that position. Reimplemented from SeqBasic.

int SeqAA::getLine (  int  y  )  [virtual]

Returns the line number for the y position. Reimplemented from SeqBasic.

int SeqAA::getMark (  int  i  )  [virtual]

Returns the mark value for a "char". Reimplemented from SeqBasic.

int SeqAA::getMarkSize (   )  [virtual]

Returns the length of the SeqPos marked part of the sequence. Reimplemented from SeqBasic.

int SeqAA::getPos (  int  i  )  [virtual]

Returns the internal ID of the "char". Reimplemented from SeqBasic.

wxRect SeqAA::getRect (  int  i  )  [virtual]

Returns the SeqPos rect for a "char". Reimplemented from SeqBasic.

int SeqAA::getRectSize (   )  [virtual]

Returns the number of SeqPos rectangles. Reimplemented from SeqBasic.

void SeqAA::initFromString (  wxString  t  )  [virtual]

Set from a string.

void SeqAA::initFromTVector (  TVector *  v  )  [virtual]

Set from a TVector class. Reimplemented from SeqBasic.

void SeqAA::logsize (   )  [virtual]

Some internal debugging thingy. Reimplemented from SeqBasic.

void SeqAA::setMark (  int  i, int  v )  [virtual]

Sets the marking of a "char". Reimplemented from SeqBasic.

void SeqAA::setPos (  int  i, int  v )  [virtual]

Sets the internal ID of the "char". Reimplemented from SeqBasic.

void SeqAA::show (  wxDC &  dc  )  [virtual]

Show. Reimplemented from SeqBasic.

void SeqAA::show_direct (  wxDC &  dc  )  [virtual]

Show quickly. Reimplemented from SeqBasic.

wxPoint SeqAA::showText (  int  ystart, wxArrayString &  tout )  [virtual]

Show as text (rarely used). Reimplemented from SeqBasic.

void SeqAA::updateProteases (   )  [virtual]

Set protease cuts in display.

bool SeqAA::useDirectRoutines (   )  [virtual]

Do we draw directly (or do we use SeqPos)? Reimplemented from SeqBasic.

virtual wxString SeqAA::whatsthis (   )  [inline, virtual]

Returns the linetype. Reimplemented from SeqBasic.

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Member Data Documentation

int SeqAA::disp

int SeqAA::mode

wxArrayTVectorItem SeqAA::offset_items

wxArrayInt SeqAA::offsets

wxString SeqAA::pa_w

wxArrayInt SeqAA::pa_wa

wxArrayTProteaseCut SeqAA::pc

List of protease cuts.

bool SeqAA::primaryMode

wxArrayTProtease SeqAA::proteases

List of proteases to look for.

bool SeqAA::showNumbers

char SeqAA::unknownAA

TVector* SeqAA::vec

Pointer to the original sequence data.

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

• C:/Programme/Dev-Cpp/Mine/GENtle/SequenceCanvas.h
• C:/Programme/Dev-Cpp/Mine/GENtle/SequenceTypeAA.cpp

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