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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

TPrimerDesignparent
wxTextCtrl * text
wxListBox * list
wxArrayString l_title
wxArrayString l_text
wxString nl

Static Private Attributes

static vector< TSantaLuciasanta_lucia = vector <TSantaLucia> ()


Detailed Description

The class implementing the PCR troubleshooting dialog.


Constructor & Destructor Documentation

PCR_troubleshoot_dialog::PCR_troubleshoot_dialog TPrimerDesign _parent,
const wxString &  title
 

Constructor.

PCR_troubleshoot_dialog::~PCR_troubleshoot_dialog  ) 
 

Destructor.


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]
 


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]
 


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