TAlignment Class Reference

The alignment module class. Note: this is actually a child class of both ChildBase and wxThreadHelper! More...

#include <Alignment.h>

Inheritance diagram for TAlignment:

List of all members.

Public Member Functions
	TAlignment (wxWindow *parent, const wxString &title)
	Constructor.
virtual	~TAlignment ()
	Destructor.
virtual void	initme ()
	Initialization.
virtual wxString	getName ()
	Returns "Alignment".
virtual void *	Entry ()
virtual int	NeedlemanWunsch (wxString &s1, wxString &s2)
	Needleman-Wunsch-align two sequences.
virtual int	SmithWaterman (wxString &s1, wxString &s2)
	Smith-Waterman-align two sequences.
virtual int	MatrixAlignment (wxString &_s1, wxString &_s2, bool local)
	Part of NW/SW alignment algorithm.
virtual void	MatrixBacktrack (vector< wxArrayInt > &back, wxString s1, wxString s2, wxString &t1, wxString &t2, int i, int j)
	Part of NW/SW alignment algorithm.
virtual void	redoAlignments (bool doRecalc=true)
	Repaint and (maybe) recalculate the alignment.
virtual void	recalcAlignments ()
	Recalculate the alignment.
virtual wxColour	findColors (char c1, char c2, bool fg)
	Generate the appropriate foreground/background color, using current settings.
virtual void	OnSettings (wxCommandEvent &ev)
	Settings button event handler.
virtual void	OnMarkAll (wxCommandEvent &ev)
	"Mark all" event handler
virtual void	OnSeqPrint (wxCommandEvent &event)
	"Print sequence" event handler
virtual void	OnFileSave (wxCommandEvent &ev)
	Save event handler.
virtual void	OnMenuBold (wxCommandEvent &ev)
	"Display bold" event handler
virtual void	OnMenuMono (wxCommandEvent &ev)
	"Display monochrome" event handler
virtual void	OnMenuNorm (wxCommandEvent &ev)
	"Display normal" event handler
virtual void	OnMenuInvs (wxCommandEvent &ev)
	"Display inverse" event handler
virtual void	OnMenuSoa (wxCommandEvent &ev)
	Some event handler.
virtual void	OnMenuSoaI (wxCommandEvent &ev)
	Some event handler.
virtual void	OnMenuSiml (wxCommandEvent &ev)
	Some event handler.
virtual void	OnMenuSeq (wxCommandEvent &ev)
	Some event handler.
virtual void	OnMenuFeat (wxCommandEvent &ev)
	Some event handler.
virtual void	OnMenuRNA (wxCommandEvent &ev)
	Some event handler.
virtual void	OnMenuCons (wxCommandEvent &ev)
	Some event handler.
virtual void	OnMenuIdent (wxCommandEvent &ev)
	Some event handler.
virtual void	OnHorizontal (wxCommandEvent &event)
	"Display horizontal" event handler
virtual void	OnCopy (wxCommandEvent &event)
	Copy event handler.
virtual void	OnFontsize (wxCommandEvent &event)
	Fontsize event handler.
virtual void	invokeOriginal (int id, int pos)
	Open the original sequence at the given position.
virtual void	callMiddleMouseButton (int id, int pos, wxString _mode=_T(""))
	Perform the middle mouse button function (the gap orgy).
virtual void	MoveUpDown (int what, int where)
	Move a line into the given direction.
virtual void	prealigned (wxArrayString &vs, wxArrayChildBase &vc)
	Initialize with a prealigned list of sequences (for example, from a multi-sequence genbank file).
virtual void	fromVector (TVector *nv)
	Initialize from a single vector (???).
virtual bool	isDNA ()
	Tries to determine wether this is a DNA or an amino acid alignment.
virtual bool	isAA ()
	Tries to determine wether this is a DNA or an amino acid alignment.
virtual void	RunPhylip (int cmd)
	Takes Phylip commands (invoked from SequenceCanvas).
virtual bool	isThreadRunning ()
	Is a thread (alignment calculation) currently running?
void	getCharMarkup (SequenceCharMarkup &scm, int vline, int pos, int vfirst)
void	editAppearance (int from, int to, int firstline, int lastline)
Public Attributes
SequenceCanvas *	sc
	Pointer to the sequence canvas.
vector< TAlignLine >	lines
	The list of TAlignLine structures.
wxColour	colDNA [256]
wxColour	colAA [256]
wxColour *	colCur
wxString	gap
wxString	matrix
wxString	consensusSequence
wxString	name
wxString	database
int	match
int	mismatch
int	gap_penalty
int	algorithm
bool	bold
bool	mono
bool	cons
bool	invs
bool	showIdentity
Protected Member Functions
virtual wxString	getExportFilters ()
virtual void	doExport (wxString filename, int filter)
	Export data, depending on filename and export type.
virtual void	readTabColors (wxString filename)
Private Member Functions
virtual void	myInsert (int line, int pos, char what)
virtual void	myDelete (int line, int pos)
virtual void	updateSequence ()
virtual void	generateConsensusSequence (bool addit=true)
virtual void	fixMenus (int i)
Private Attributes
wxChoice *	mmb
SeqAA *	aaa
bool	threadRunning
bool	keepIdentity
wxChoice *	fontsize

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Detailed Description

The alignment module class. Note: this is actually a child class of both ChildBase and wxThreadHelper!

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Constructor & Destructor Documentation

TAlignment::TAlignment (  wxWindow *  parent, const wxString &  title )

Constructor.

TAlignment::~TAlignment (   )  [virtual]

Destructor.

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Member Function Documentation

void TAlignment::callMiddleMouseButton (  int  id, int  pos, wxString  _mode = _T("") )  [virtual]

Perform the middle mouse button function (the gap orgy).

void TAlignment::doExport (  wxString  filename, int  filter )  [protected, virtual]

Export data, depending on filename and export type. Reimplemented from ChildBase.

void TAlignment::editAppearance (  int  from, int  to, int  firstline, int  lastline )

void * TAlignment::Entry (   )  [virtual]

wxColour TAlignment::findColors (  char  c1, char  c2, bool  fg )  [virtual]

Generate the appropriate foreground/background color, using current settings.

void TAlignment::fixMenus (  int  i  )  [private, virtual]

void TAlignment::fromVector (  TVector *  nv  )  [virtual]

Initialize from a single vector (???).

void TAlignment::generateConsensusSequence (  bool  addit = true  )  [private, virtual]

void TAlignment::getCharMarkup (  SequenceCharMarkup &  scm, int  vline, int  pos, int  vfirst )

wxString TAlignment::getExportFilters (   )  [protected, virtual]

Reimplemented from ChildBase.

wxString TAlignment::getName (   )  [virtual]

Returns "Alignment". Reimplemented from ChildBase.

void TAlignment::initme (   )  [virtual]

Initialization.

void TAlignment::invokeOriginal (  int  id, int  pos )  [virtual]

Open the original sequence at the given position.

bool TAlignment::isAA (   )  [virtual]

Tries to determine wether this is a DNA or an amino acid alignment.

bool TAlignment::isDNA (   )  [virtual]

Tries to determine wether this is a DNA or an amino acid alignment.

virtual bool TAlignment::isThreadRunning (   )  [inline, virtual]

Is a thread (alignment calculation) currently running?

int TAlignment::MatrixAlignment (  wxString &  _s1, wxString &  _s2, bool  local )  [virtual]

Part of NW/SW alignment algorithm.

void TAlignment::MatrixBacktrack (  vector< wxArrayInt > &  back, wxString  s1, wxString  s2, wxString &  t1, wxString &  t2, int  i, int  j )  [virtual]

Part of NW/SW alignment algorithm.

void TAlignment::MoveUpDown (  int  what, int  where )  [virtual]

Move a line into the given direction.

void TAlignment::myDelete (  int  line, int  pos )  [private, virtual]

void TAlignment::myInsert (  int  line, int  pos, char  what )  [private, virtual]

int TAlignment::NeedlemanWunsch (  wxString &  s1, wxString &  s2 )  [virtual]

Needleman-Wunsch-align two sequences.

void TAlignment::OnCopy (  wxCommandEvent &  event  )  [virtual]

Copy event handler.

void TAlignment::OnFileSave (  wxCommandEvent &  ev  )  [virtual]

Save event handler.

void TAlignment::OnFontsize (  wxCommandEvent &  event  )  [virtual]

Fontsize event handler.

void TAlignment::OnHorizontal (  wxCommandEvent &  event  )  [virtual]

"Display horizontal" event handler

void TAlignment::OnMarkAll (  wxCommandEvent &  ev  )  [virtual]

"Mark all" event handler

void TAlignment::OnMenuBold (  wxCommandEvent &  ev  )  [virtual]

"Display bold" event handler

void TAlignment::OnMenuCons (  wxCommandEvent &  ev  )  [virtual]

Some event handler.

void TAlignment::OnMenuFeat (  wxCommandEvent &  ev  )  [virtual]

Some event handler.

void TAlignment::OnMenuIdent (  wxCommandEvent &  ev  )  [virtual]

Some event handler.

void TAlignment::OnMenuInvs (  wxCommandEvent &  ev  )  [virtual]

"Display inverse" event handler

void TAlignment::OnMenuMono (  wxCommandEvent &  ev  )  [virtual]

"Display monochrome" event handler

void TAlignment::OnMenuNorm (  wxCommandEvent &  ev  )  [virtual]

"Display normal" event handler

void TAlignment::OnMenuRNA (  wxCommandEvent &  ev  )  [virtual]

Some event handler.

void TAlignment::OnMenuSeq (  wxCommandEvent &  ev  )  [virtual]

Some event handler.

void TAlignment::OnMenuSiml (  wxCommandEvent &  ev  )  [virtual]

Some event handler.

void TAlignment::OnMenuSoa (  wxCommandEvent &  ev  )  [virtual]

Some event handler.

void TAlignment::OnMenuSoaI (  wxCommandEvent &  ev  )  [virtual]

Some event handler.

void TAlignment::OnSeqPrint (  wxCommandEvent &  event  )  [virtual]

"Print sequence" event handler

void TAlignment::OnSettings (  wxCommandEvent &  ev  )  [virtual]

Settings button event handler.

void TAlignment::prealigned (  wxArrayString &  vs, wxArrayChildBase &  vc )  [virtual]

Initialize with a prealigned list of sequences (for example, from a multi-sequence genbank file).

void TAlignment::readTabColors (  wxString  filename  )  [protected, virtual]

void TAlignment::recalcAlignments (   )  [virtual]

Recalculate the alignment.

void TAlignment::redoAlignments (  bool  doRecalc = true  )  [virtual]

Repaint and (maybe) recalculate the alignment.

void TAlignment::RunPhylip (  int  cmd  )  [virtual]

Takes Phylip commands (invoked from SequenceCanvas).

int TAlignment::SmithWaterman (  wxString &  s1, wxString &  s2 )  [virtual]

Smith-Waterman-align two sequences.

void TAlignment::updateSequence (   )  [private, virtual]

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Member Data Documentation

SeqAA* TAlignment::aaa [private]

int TAlignment::algorithm

bool TAlignment::bold

wxColour TAlignment::colAA[256]

wxColour * TAlignment::colCur

wxColour TAlignment::colDNA[256]

bool TAlignment::cons

wxString TAlignment::consensusSequence

wxString TAlignment::database

wxChoice* TAlignment::fontsize [private]

wxString TAlignment::gap

int TAlignment::gap_penalty

bool TAlignment::invs

bool TAlignment::keepIdentity [private]

vector<TAlignLine> TAlignment::lines

The list of TAlignLine structures.

int TAlignment::match

wxString TAlignment::matrix

int TAlignment::mismatch

wxChoice* TAlignment::mmb [private]

bool TAlignment::mono

wxString TAlignment::name

SequenceCanvas* TAlignment::sc

Pointer to the sequence canvas.

bool TAlignment::showIdentity

bool TAlignment::threadRunning [private]

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

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

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