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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:

ChildBase 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

SequenceCanvassc
 Pointer to the sequence canvas.
vector< TAlignLinelines
 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
SeqAAaaa
bool threadRunning
bool keepIdentity
wxChoice * fontsize

Detailed Description

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


Constructor & Destructor Documentation

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

Constructor.

TAlignment::~TAlignment  )  [virtual]
 

Destructor.


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]
 


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]
 


The documentation for this class was generated from the following files:
Generated on Fri Aug 11 16:19:46 2006 for GENtle by  doxygen 1.4.1