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/** \file
\brief The TPrimer class
*/
#ifndef _TPRIMER_H_
#define _TPRIMER_H_
#include "main.h"
#include "ChildBase.h"
#include <wx/splitter.h>
class TVector ;
class TPrimerDialog ;
class TPrimerDesign ;
/** \def TM_STANDARD
\brief Standard (nearest neighbour) method */
#define TM_STANDARD 0
/** \def TM_SALT
\brief Salt-adjusted method */
#define TM_SALT 1
/** \def TM_GC
\brief GC method */
#define TM_GC 2
/// This class holds and generates information about a primer
class TPrimer
{
public :
TPrimer ( int _from = 0 , int _to = 0 , bool _upper = true ) ; ///< Constructor
~TPrimer () {} ; ///< Dummy Destructor
void getSequenceFromVector ( TVector *v , bool from3 = false ) ; ///< Reads primer sequence from vectors
void makeStats () ; ///< Generates key values about the primer
void evaluate ( float tm_opt = 0 ) ; ///< Evaluates primer
wxString report () ; ///< Generates a human-readable report
wxString get53sequence () ; ///< Returns the 5'->3' primer sequence
wxString get35sequence () ; ///< Returns the 3'->5' primer sequence
int checkFit ( TVector *v , bool justCount = false ) ; ///< Tries to fit the primer to a sequence
bool overlap ( TPrimer &op ) ; ///< Does this primer overlap with another?
float getTm ( int type = TM_STANDARD ) ; ///< Get melting temperature
float getEvaluation () ; ///< Get quality evaluation (for annealing)
float getGCcontents () ; ///< Get GC contents
wxString getName () ; ///< Returns the name of the primer, if any was given
void setName ( wxString nn ) ; ///< Sets the name of the primer
// Variables
/// The beginning of the primer in a sequence
int from , to ; ///< The end of a primer in the sequence
wxString sequence ; ///< The primer sequence
bool upper ; ///< Upper (5'->3') or lower (3'->5') primer?
TVector *annealingVector ; ///< The vector to anneal to
private :
void evaluateSelfAnnealing () ; ///< Check for self-annealing
float evaluateTm ( double conc_nm = 50 , double Na_mm = 50 ) ; ///< Calculate melting temperature, salt-adjusted
void OligoCount () ; ///< Nearest neighbour helper method
double NeighbourTM ( bool max , double pconc , double saltconc ) ; ///< Calculate melting temperature, nearest neighbour
bool IsBase ( wxString theBase ) ; ///< Nearest neighbour helper method
bool IsIUpacBase ( wxString theBase ) ; ///< Nearest neighbour helper method
double *CalcIUpair ( wxString base0 , wxString base , int i , bool max ) ; ///< Nearest neighbour helper method
double DeltaG ( bool max ) ; ///< Nearest neighbour helper method
double DeltaH ( bool max ) ; ///< Nearest neighbour helper method
double DeltaS ( bool max ) ; ///< Nearest neighbour helper method
double CountNeighbors ( wxString s ) ; ///< Nearest neighbour helper method
void invertSequence() ; ///< Inverts the sequence
wxString getAnnealingSequence() ; ///< Returns annealing sequence
// Variables
wxString name ;
int contents[256] ;
float pgc ; ///< GC%
float evaluation ; ///< The last quality evaluation
float tm ; ///< Melting temperature, nearest neighbour method
float tm_salt ; ///< Melting temperature, salt-adjusted
float tm_gc ; ///< Melting temperature, GC method
wxString ann1 , ann2 , annm ;
int annScore ; ///< Annealing score
double S , H ;
double IUpairVals_min[3] , IUpairVals_max[3] ;
double deltaHValmin , deltaHValmax ;
double deltaSValmin , deltaSValmax ;
double deltaGValmin , deltaGValmax ;
double aaCount, atCount , taCount , caCount , gtCount ;
double ctCount , gaCount , cgCount , gcCount , ggCount ;
} ;
#endif
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