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MyChild Class Reference

The very, very, *very* important module to handle DNA in all its beauty! More...

#include <MyChild.h>

Inheritance diagram for MyChild:

ChildBase List of all members.

Public Member Functions

 MyChild (wxWindow *parent, const wxString &title, const wxPoint &pos, const wxSize &size, const long style)
 Constructor.
 ~MyChild ()
 Destructor.
virtual void OnAA_none (wxCommandEvent &event)
 "Display no amino acids" event handler
virtual void OnAA_known (wxCommandEvent &event)
 "Display only known amino acids" event handler
virtual void OnAA_all (wxCommandEvent &event)
 "Display amino acids for all reading frames" event handler
virtual void OnAA_three (wxCommandEvent &event)
 "Display three-letter amino acids" event handler
virtual void OnAA_one (wxCommandEvent &event)
 "Display one-letter amino acids" event handler
virtual void OnAA_three_1 (wxCommandEvent &event)
 "Display amino acids, reading frame 1" event handler
virtual void OnAA_three_2 (wxCommandEvent &event)
 "Display amino acids, reading frame 2" event handler
virtual void OnAA_three_3 (wxCommandEvent &event)
 "Display amino acids, reading frame 3" event handler
virtual void OnAA_three_M1 (wxCommandEvent &event)
 "Display amino acids, reading frame -1" event handler
virtual void OnAA_three_M2 (wxCommandEvent &event)
 "Display amino acids, reading frame -2" event handler
virtual void OnAA_three_M3 (wxCommandEvent &event)
 "Display amino acids, reading frame -3" event handler
virtual void OnAA_setit (int mode)
 Sets the amino acid display mode (called by the OnAA_ event handlers).
virtual void OnActivate (wxActivateEvent &event)
 Activation event handler.
virtual void Undo (wxCommandEvent &event)
 Undo event handler.
virtual void Redo (wxCommandEvent &event)
 Redo event handler (not implemented).
virtual void updateUndoMenu ()
 Updates the undo menu item.
virtual void OnMarkAll (wxCommandEvent &event)
 "Mark all" (Ctrl-A) event handler
virtual void OnTransformSequence (wxCommandEvent &event)
 "Transform sequence" event handler
virtual void OnExtractAA (wxCommandEvent &event)
 "Extract amino acids" event handler
virtual void OnFind (wxCommandEvent &event)
 "Find" event handler
virtual void OnFileSave (wxCommandEvent &WXUNUSED(event))
 "Save"/"Store" event handler
virtual void OnQuit (wxCommandEvent &event)
 "Quit" event handler
virtual void OnCut (wxCommandEvent &event)
 Cut event handler.
virtual void OnCopy (wxCommandEvent &event)
 Copy event handler.
virtual void OnPaste (wxCommandEvent &event)
 Paste event handler.
virtual void OnViewMode (wxCommandEvent &event)
 Switch to fullscreen plasmid map event handler.
virtual void OnEditMode (wxCommandEvent &event)
 Sqitch to edit mode event handler.
virtual void OnCircularLinear (wxCommandEvent &event)
 Toggle circular/linear event handler.
virtual void OnCopyToNew (wxCommandEvent &event)
 "Copy as new sequence" event handler
virtual void OnAsNewFeature (wxCommandEvent &event)
 "Selection as new feature" event handler
virtual void OnPrintImage (wxCommandEvent &event)
 Print image event handler.
virtual void OnPrintRestrictionList (wxCommandEvent &event)
 Print restriction list event handler.
virtual void OnRestriction (wxCommandEvent &event)
 Restriction event handler.
virtual void OnHelp (wxCommandEvent &event)
 Help event handler.
virtual void OnORFs (wxCommandEvent &event)
 "Show/hide open reading frames" event handler
virtual void OnEditORFs (wxCommandEvent &event)
 Change open reading frame settings event handler.
virtual void OnSeqPrint (wxCommandEvent &event)
 Print sequence event handler.
virtual void OnPrintReport (wxCommandEvent &event)
 "Print report" event handler
virtual void OnToggleFeatures (wxCommandEvent &event)
 Feature display on/off event handler.
virtual void OnToggleRestriction (wxCommandEvent &event)
 "Restriction enzymes in sequence on/off" event handler
virtual void OnToggleIDNA (wxCommandEvent &event)
 Inverse DNA display event handler.
virtual void OnRunPCR (wxCommandEvent &event)
 PCR event handler.
virtual void OnZoom (wxCommandEvent &ev)
 Zoom event handler.
virtual void OnUpdateRefresh (wxUpdateUIEvent &event)
 Update/Refresh event handler.
virtual void OnSequencingPrimer (wxCommandEvent &WXUNUSED(event))
 "Find sequencing primers" event handler
virtual void OnRemoveSequencingPrimers (wxCommandEvent &WXUNUSED(event))
 "Remove sequencing primers" event handler
virtual void OnAutoAnnotate (wxCommandEvent &WXUNUSED(event))
 Automatic annotation event handler.
virtual void OnSpeak (wxCommandEvent &WXUNUSED(event))
 Speak sequence event handler.
virtual void OnSiRNA (wxCommandEvent &WXUNUSED(event))
 siRNA event handler
virtual void OnFontsize (wxCommandEvent &event)
 Fontsize event handler.
virtual void OnDummy (wxCommandEvent &WXUNUSED(event))
virtual void initme ()
 Initializes the module.
virtual void initPanels ()
 Initializes the panels.
virtual wxString getName ()
 Returns the module name.
virtual void EnforceRefesh ()
 Force display refresh.
virtual void updateSequenceCanvas (bool remember=false)
 Refresh the sequence display.
virtual wxString doExtractAA (bool coding=true)
 Extract amino acid sequence from DNA.
virtual bool runRestriction (wxString s)
 Run the restriction.
virtual void addFragmentsToGel (wxString title, wxArrayInt &cuts, TVirtualGel *gel, TRestrictionEditor &ed, bool partial)
 Add restriction fragments to gel.
virtual MyChild * doTransformSequence (bool inNewVector, bool complement, bool invers)
 Transform the sequence.

Public Attributes

TVectorTree * treeBox
 Pointer to the sequence properties tree structure.
TURLtext * propBox
 Pointer to the properties text box.
PlasmidCanvas * cPlasmid
 Pointer to the plasmid canvas.
MySplitter * sw
MySplitter * swu
MySplitter * swl
bool showORFs
bool viewMode
int sp1
int sp2
int aa_offset
int ly
int aa_state
int aa_disp
int orf_mode

Protected Member Functions

virtual void updateToolbar ()
 Set the toolbar of this module.
virtual void initToolbar ()
 Setup the toolbar for this module.
virtual void initMenus ()
 Initialize the menus.
void add_siRNA (int item)
int add_siRNA_sub (wxString s, int pos)

Protected Attributes

wxChoice * fontsize

Detailed Description

The very, very, *very* important module to handle DNA in all its beauty!

Constructor & Destructor Documentation

MyChild::MyChild (  wxWindow *  parent,
const wxString &  title,
const wxPoint &  pos,
const wxSize &  size,
const long  style
) 
 

Constructor.

MyChild::~MyChild (   ) 
 

Destructor.

Member Function Documentation

void MyChild::add_siRNA (  int  item  )  [protected]
 

int MyChild::add_siRNA_sub (  wxString  s,
int  pos
)  [protected]
 

void MyChild::addFragmentsToGel (  wxString  title,
wxArrayInt &  cuts,
TVirtualGel *  gel,
TRestrictionEditor &  ed,
bool  partial
)  [virtual]
 

Add restriction fragments to gel.

wxString MyChild::doExtractAA (  bool  coding = true  )  [virtual]
 

Extract amino acid sequence from DNA.

MyChild * MyChild::doTransformSequence (  bool  inNewVector,
bool  complement,
bool  invers
)  [virtual]
 

Transform the sequence.

void MyChild::EnforceRefesh (   )  [virtual]
 

Force display refresh.

Reimplemented from ChildBase.

wxString MyChild::getName (   )  [virtual]
 

Returns the module name.

Reimplemented from ChildBase.

void MyChild::initme (   )  [virtual]
 

Initializes the module.

void MyChild::initMenus (   )  [protected, virtual]
 

Initialize the menus.

void MyChild::initPanels (   )  [virtual]
 

Initializes the panels.

void MyChild::initToolbar (   )  [protected, virtual]
 

Setup the toolbar for this module.

void MyChild::OnAA_all (  wxCommandEvent &  event  )  [virtual]
 

"Display amino acids for all reading frames" event handler

void MyChild::OnAA_known (  wxCommandEvent &  event  )  [virtual]
 

"Display only known amino acids" event handler

void MyChild::OnAA_none (  wxCommandEvent &  event  )  [virtual]
 

"Display no amino acids" event handler

void MyChild::OnAA_one (  wxCommandEvent &  event  )  [virtual]
 

"Display one-letter amino acids" event handler

void MyChild::OnAA_setit (  int  mode  )  [virtual]
 

Sets the amino acid display mode (called by the OnAA_ event handlers).

void MyChild::OnAA_three (  wxCommandEvent &  event  )  [virtual]
 

"Display three-letter amino acids" event handler

void MyChild::OnAA_three_1 (  wxCommandEvent &  event  )  [virtual]
 

"Display amino acids, reading frame 1" event handler

void MyChild::OnAA_three_2 (  wxCommandEvent &  event  )  [virtual]
 

"Display amino acids, reading frame 2" event handler

void MyChild::OnAA_three_3 (  wxCommandEvent &  event  )  [virtual]
 

"Display amino acids, reading frame 3" event handler

void MyChild::OnAA_three_M1 (  wxCommandEvent &  event  )  [virtual]
 

"Display amino acids, reading frame -1" event handler

void MyChild::OnAA_three_M2 (  wxCommandEvent &  event  )  [virtual]
 

"Display amino acids, reading frame -2" event handler

void MyChild::OnAA_three_M3 (  wxCommandEvent &  event  )  [virtual]
 

"Display amino acids, reading frame -3" event handler

void MyChild::OnActivate (  wxActivateEvent &  event  )  [virtual]
 

Activation event handler.

void MyChild::OnAsNewFeature (  wxCommandEvent &  event  )  [virtual]
 

"Selection as new feature" event handler

virtual void MyChild::OnAutoAnnotate (  wxCommandEvent &  WXUNUSED(event)  )  [virtual]
 

Automatic annotation event handler.

void MyChild::OnCircularLinear (  wxCommandEvent &  event  )  [virtual]
 

Toggle circular/linear event handler.

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

Copy event handler.

void MyChild::OnCopyToNew (  wxCommandEvent &  event  )  [virtual]
 

"Copy as new sequence" event handler

void MyChild::OnCut (  wxCommandEvent &  event  )  [virtual]
 

Cut event handler.

virtual void MyChild::OnDummy (  wxCommandEvent &  WXUNUSED(event)  )  [inline, virtual]
 

Reimplemented from ChildBase.

void MyChild::OnEditMode (  wxCommandEvent &  event  )  [virtual]
 

Sqitch to edit mode event handler.

void MyChild::OnEditORFs (  wxCommandEvent &  event  )  [virtual]
 

Change open reading frame settings event handler.

void MyChild::OnExtractAA (  wxCommandEvent &  event  )  [virtual]
 

"Extract amino acids" event handler

void MyChild::OnFileSave (  wxCommandEvent &  WXUNUSED(event)  )  [virtual]
 

"Save"/"Store" event handler

Reimplemented from ChildBase.

void MyChild::OnFind (  wxCommandEvent &  event  )  [virtual]
 

"Find" event handler

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

Fontsize event handler.

void MyChild::OnHelp (  wxCommandEvent &  event  )  [virtual]
 

Help event handler.

void MyChild::OnMarkAll (  wxCommandEvent &  event  )  [virtual]
 

"Mark all" (Ctrl-A) event handler

void MyChild::OnORFs (  wxCommandEvent &  event  )  [virtual]
 

"Show/hide open reading frames" event handler

void MyChild::OnPaste (  wxCommandEvent &  event  )  [virtual]
 

Paste event handler.

void MyChild::OnPrintImage (  wxCommandEvent &  event  )  [virtual]
 

Print image event handler.

void MyChild::OnPrintReport (  wxCommandEvent &  event  )  [virtual]
 

"Print report" event handler

void MyChild::OnPrintRestrictionList (  wxCommandEvent &  event  )  [virtual]
 

Print restriction list event handler.

virtual void MyChild::OnQuit (  wxCommandEvent &  event  )  [virtual]
 

"Quit" event handler

virtual void MyChild::OnRemoveSequencingPrimers (  wxCommandEvent &  WXUNUSED(event)  )  [virtual]
 

"Remove sequencing primers" event handler

void MyChild::OnRestriction (  wxCommandEvent &  event  )  [virtual]
 

Restriction event handler.

void MyChild::OnRunPCR (  wxCommandEvent &  event  )  [virtual]
 

PCR event handler.

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

Print sequence event handler.

virtual void MyChild::OnSequencingPrimer (  wxCommandEvent &  WXUNUSED(event)  )  [virtual]
 

"Find sequencing primers" event handler

virtual void MyChild::OnSiRNA (  wxCommandEvent &  WXUNUSED(event)  )  [virtual]
 

siRNA event handler

virtual void MyChild::OnSpeak (  wxCommandEvent &  WXUNUSED(event)  )  [virtual]
 

Speak sequence event handler.

void MyChild::OnToggleFeatures (  wxCommandEvent &  event  )  [virtual]
 

Feature display on/off event handler.

void MyChild::OnToggleIDNA (  wxCommandEvent &  event  )  [virtual]
 

Inverse DNA display event handler.

void MyChild::OnToggleRestriction (  wxCommandEvent &  event  )  [virtual]
 

"Restriction enzymes in sequence on/off" event handler

void MyChild::OnTransformSequence (  wxCommandEvent &  event  )  [virtual]
 

"Transform sequence" event handler

void MyChild::OnUpdateRefresh (  wxUpdateUIEvent &  event  )  [virtual]
 

Update/Refresh event handler.

void MyChild::OnViewMode (  wxCommandEvent &  event  )  [virtual]
 

Switch to fullscreen plasmid map event handler.

void MyChild::OnZoom (  wxCommandEvent &  ev  )  [virtual]
 

Zoom event handler.

void MyChild::Redo (  wxCommandEvent &  event  )  [virtual]
 

Redo event handler (not implemented).

bool MyChild::runRestriction (  wxString  s  )  [virtual]
 

Run the restriction.

void MyChild::Undo (  wxCommandEvent &  event  )  [virtual]
 

Undo event handler.

void MyChild::updateSequenceCanvas (  bool  remember = false  )  [virtual]
 

Refresh the sequence display.

Reimplemented from ChildBase.

void MyChild::updateToolbar (   )  [protected, virtual]
 

Set the toolbar of this module.

Reimplemented from ChildBase.

void MyChild::updateUndoMenu (   )  [virtual]
 

Updates the undo menu item.

Reimplemented from ChildBase.

Member Data Documentation

int MyChild::aa_disp
 

int MyChild::aa_offset
 

int MyChild::aa_state
 

PlasmidCanvas* MyChild::cPlasmid
 

Pointer to the plasmid canvas.

wxChoice* MyChild::fontsize [protected]
 

int MyChild::ly
 

int MyChild::orf_mode
 

TURLtext* MyChild::propBox
 

Pointer to the properties text box.

bool MyChild::showORFs
 

int MyChild::sp1
 

int MyChild::sp2
 

MySplitter* MyChild::sw
 

MySplitter * MyChild::swl
 

MySplitter * MyChild::swu
 

TVectorTree* MyChild::treeBox
 

Pointer to the sequence properties tree structure.

bool MyChild::viewMode
 

The documentation for this class was generated from the following files:
Generated on Fri Aug 11 16:19:44 2006 for GENtle by  doxygen 1.4.1