PCR_troubleshoot_dialog Class Reference

The class implementing the PCR troubleshooting dialog. More...

#include <PCR_Troubleshoot.h>

List of all members.

Public Member Functions
	PCR_troubleshoot_dialog (TPrimerDesign *_parent, const wxString &title)
	Constructor.
	~PCR_troubleshoot_dialog ()
	Destructor.
virtual void	OnOK (wxCommandEvent &ev)
	OK button event handler.
virtual void	OnCancel (wxCommandEvent &ev)
	Cancel button event handler.
virtual void	OnList (wxCommandEvent &ev)
	List event handler.
virtual void	OnCharHook (wxKeyEvent &event)
	Key event handler.
Private Member Functions
virtual void	scan ()
	Performs various scans.
virtual void	scan_hairpin (TPrimer &p, int nr)
	Scans for hairpins.
virtual void	scan_dimer (TPrimer &p1, TPrimer &p2, int nr1, int nr2)
	Scans for (self-)dimers.
virtual void	scan_length (TPrimer &p, int nr)
	Checks primer length.
virtual void	scan_GCcontent (TPrimer &p, int nr)
	Checks primer GC contents.
virtual void	scan_GCclamp (TPrimer &p, int nr)
	Checks for GC clamp.
virtual void	scan_end_stability (TPrimer &p, int nr)
	Checks primer end stability.
virtual void	scan_Runs (TPrimer &p, int nr, int length)
virtual void	scan_specificity (TPrimer &p, int nr)
	Checks primer specificity.
virtual void	scan_melting_temperature (TPrimer &p, int nr)
	Checks melting temperature.
virtual void	add_warning (TPrimer &p, int nr, wxString head, wxString tail)
	Adds a warning to the list.
virtual void	add_error (TPrimer &p, int nr, wxString head, wxString tail)
	Adds an error to the list.
virtual void	show_item (int n)
virtual wxString	invert (wxString s)
	Inverts a (DNA) sequence.
virtual wxString	trim_both (wxString s1, wxString s2, wxString s3)
virtual wxArrayString	get_matrix (wxString s1, wxString s2)
virtual wxArrayString	get_matches (wxArrayString &m, int min, int allowed_gaps=0)
virtual void	fillSantaLucia ()
virtual wxChar	opp (wxChar c)
wxString	get_dimer_connections (wxString s1, wxString s2)
virtual double	deltaG0_dimer (wxString s1, wxString s2)
virtual double	deltaG0 (TPrimer &p)
virtual double	deltaH0 (TPrimer &p)
virtual double	deltaS0 (TPrimer &p)
virtual int	getSLindex (wxString s)
Private Attributes
TPrimerDesign *	parent
wxTextCtrl *	text
wxListBox *	list
wxArrayString	l_title
wxArrayString	l_text
wxString	nl
Static Private Attributes
static vector< TSantaLucia >	santa_lucia = vector <TSantaLucia> ()

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Detailed Description

The class implementing the PCR troubleshooting dialog.

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Constructor & Destructor Documentation

PCR_troubleshoot_dialog::PCR_troubleshoot_dialog (  TPrimerDesign *  _parent, const wxString &  title )

Constructor.

PCR_troubleshoot_dialog::~PCR_troubleshoot_dialog (   )

Destructor.

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Member Function Documentation

void PCR_troubleshoot_dialog::add_error (  TPrimer &  p, int  nr, wxString  head, wxString  tail )  [private, virtual]

Adds an error to the list.

void PCR_troubleshoot_dialog::add_warning (  TPrimer &  p, int  nr, wxString  head, wxString  tail )  [private, virtual]

Adds a warning to the list.

double PCR_troubleshoot_dialog::deltaG0 (  TPrimer &  p  )  [private, virtual]

double PCR_troubleshoot_dialog::deltaG0_dimer (  wxString  s1, wxString  s2 )  [private, virtual]

double PCR_troubleshoot_dialog::deltaH0 (  TPrimer &  p  )  [private, virtual]

double PCR_troubleshoot_dialog::deltaS0 (  TPrimer &  p  )  [private, virtual]

void PCR_troubleshoot_dialog::fillSantaLucia (   )  [private, virtual]

wxString PCR_troubleshoot_dialog::get_dimer_connections (  wxString  s1, wxString  s2 )  [private]

wxArrayString PCR_troubleshoot_dialog::get_matches (  wxArrayString &  m, int  min, int  allowed_gaps = 0 )  [private, virtual]

wxArrayString PCR_troubleshoot_dialog::get_matrix (  wxString  s1, wxString  s2 )  [private, virtual]

int PCR_troubleshoot_dialog::getSLindex (  wxString  s  )  [private, virtual]

wxString PCR_troubleshoot_dialog::invert (  wxString  s  )  [private, virtual]

Inverts a (DNA) sequence.

void PCR_troubleshoot_dialog::OnCancel (  wxCommandEvent &  ev  )  [virtual]

Cancel button event handler.

void PCR_troubleshoot_dialog::OnCharHook (  wxKeyEvent &  event  )  [virtual]

Key event handler.

void PCR_troubleshoot_dialog::OnList (  wxCommandEvent &  ev  )  [virtual]

List event handler.

void PCR_troubleshoot_dialog::OnOK (  wxCommandEvent &  ev  )  [virtual]

OK button event handler.

wxChar PCR_troubleshoot_dialog::opp (  wxChar  c  )  [private, virtual]

void PCR_troubleshoot_dialog::scan (   )  [private, virtual]

Performs various scans.

void PCR_troubleshoot_dialog::scan_dimer (  TPrimer &  p1, TPrimer &  p2, int  nr1, int  nr2 )  [private, virtual]

Scans for (self-)dimers.

void PCR_troubleshoot_dialog::scan_end_stability (  TPrimer &  p, int  nr )  [private, virtual]

Checks primer end stability.

void PCR_troubleshoot_dialog::scan_GCclamp (  TPrimer &  p, int  nr )  [private, virtual]

Checks for GC clamp.

void PCR_troubleshoot_dialog::scan_GCcontent (  TPrimer &  p, int  nr )  [private, virtual]

Checks primer GC contents.

void PCR_troubleshoot_dialog::scan_hairpin (  TPrimer &  p, int  nr )  [private, virtual]

Scans for hairpins.

void PCR_troubleshoot_dialog::scan_length (  TPrimer &  p, int  nr )  [private, virtual]

Checks primer length.

void PCR_troubleshoot_dialog::scan_melting_temperature (  TPrimer &  p, int  nr )  [private, virtual]

Checks melting temperature.

void PCR_troubleshoot_dialog::scan_Runs (  TPrimer &  p, int  nr, int  length )  [private, virtual]

void PCR_troubleshoot_dialog::scan_specificity (  TPrimer &  p, int  nr )  [private, virtual]

Checks primer specificity.

void PCR_troubleshoot_dialog::show_item (  int  n  )  [private, virtual]

wxString PCR_troubleshoot_dialog::trim_both (  wxString  s1, wxString  s2, wxString  s3 )  [private, virtual]

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Member Data Documentation

wxArrayString PCR_troubleshoot_dialog::l_text [private]

wxArrayString PCR_troubleshoot_dialog::l_title [private]

wxListBox* PCR_troubleshoot_dialog::list [private]

wxString PCR_troubleshoot_dialog::nl [private]

TPrimerDesign* PCR_troubleshoot_dialog::parent [private]

vector< TSantaLucia > PCR_troubleshoot_dialog::santa_lucia = vector <TSantaLucia> () [static, private]

wxTextCtrl* PCR_troubleshoot_dialog::text [private]

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

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

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