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TPrimer Class Reference

This class holds and generates information about a primer. More...

#include <TPrimer.h>

List of all members.

Public Member Functions

 TPrimer (int _from=0, int _to=0, bool _upper=true)
 Constructor.
 ~TPrimer ()
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.

Public Attributes

int from
 The beginning of the primer in a sequence.
int to
 The end of a primer in the sequence.
wxString sequence
 The primer sequence.
bool upper
 Upper (5'->3') or lower (3'->5') primer?
TVectorannealingVector
 The vector to anneal to.

Private Member Functions

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.

Private Attributes

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
wxString ann2
wxString annm
int annScore
 Annealing score.
double S
double H
double IUpairVals_min [3]
double IUpairVals_max [3]
double deltaHValmin
double deltaHValmax
double deltaSValmin
double deltaSValmax
double deltaGValmin
double deltaGValmax
double aaCount
double atCount
double taCount
double caCount
double gtCount
double ctCount
double gaCount
double cgCount
double gcCount
double ggCount


Detailed Description

This class holds and generates information about a primer.


Constructor & Destructor Documentation

TPrimer::TPrimer int  _from = 0,
int  _to = 0,
bool  _upper = true
 

Constructor.

TPrimer::~TPrimer  )  [inline]
 


Member Function Documentation

double * TPrimer::CalcIUpair wxString  base0,
wxString  base,
int  i,
bool  max
[private]
 

Nearest neighbour helper method.

int TPrimer::checkFit TVector v,
bool  justCount = false
 

Tries to fit the primer to a sequence.

double TPrimer::CountNeighbors wxString  s  )  [private]
 

Nearest neighbour helper method.

double TPrimer::DeltaG bool  max  )  [private]
 

Nearest neighbour helper method.

double TPrimer::DeltaH bool  max  )  [private]
 

Nearest neighbour helper method.

double TPrimer::DeltaS bool  max  )  [private]
 

Nearest neighbour helper method.

void TPrimer::evaluate float  tm_opt = 0  ) 
 

Evaluates primer.

void TPrimer::evaluateSelfAnnealing  )  [private]
 

Check for self-annealing.

float TPrimer::evaluateTm double  conc_nm = 50,
double  Na_mm = 50
[private]
 

Calculate melting temperature, salt-adjusted.

wxString TPrimer::get35sequence  ) 
 

Returns the 3'->5' primer sequence.

wxString TPrimer::get53sequence  ) 
 

Returns the 5'->3' primer sequence.

wxString TPrimer::getAnnealingSequence  )  [private]
 

Returns annealing sequence.

float TPrimer::getEvaluation  ) 
 

Get quality evaluation (for annealing).

float TPrimer::getGCcontents  ) 
 

Get GC contents.

wxString TPrimer::getName  ) 
 

Returns the name of the primer, if any was given.

void TPrimer::getSequenceFromVector TVector v,
bool  from3 = false
 

Reads primer sequence from vectors.

float TPrimer::getTm int  type = TM_STANDARD  ) 
 

Get melting temperature.

void TPrimer::invertSequence  )  [private]
 

Inverts the sequence.

bool TPrimer::IsBase wxString  theBase  )  [private]
 

Nearest neighbour helper method.

bool TPrimer::IsIUpacBase wxString  theBase  )  [private]
 

Nearest neighbour helper method.

void TPrimer::makeStats  ) 
 

Generates key values about the primer.

double TPrimer::NeighbourTM bool  max,
double  pconc,
double  saltconc
[private]
 

Calculate melting temperature, nearest neighbour.

void TPrimer::OligoCount  )  [private]
 

Nearest neighbour helper method.

bool TPrimer::overlap TPrimer op  ) 
 

Does this primer overlap with another?

wxString TPrimer::report  ) 
 

Generates a human-readable report.

void TPrimer::setName wxString  nn  ) 
 

Sets the name of the primer.


Member Data Documentation

double TPrimer::aaCount [private]
 

wxString TPrimer::ann1 [private]
 

wxString TPrimer::ann2 [private]
 

TVector* TPrimer::annealingVector
 

The vector to anneal to.

wxString TPrimer::annm [private]
 

int TPrimer::annScore [private]
 

Annealing score.

double TPrimer::atCount [private]
 

double TPrimer::caCount [private]
 

double TPrimer::cgCount [private]
 

int TPrimer::contents[256] [private]
 

double TPrimer::ctCount [private]
 

double TPrimer::deltaGValmax [private]
 

double TPrimer::deltaGValmin [private]
 

double TPrimer::deltaHValmax [private]
 

double TPrimer::deltaHValmin [private]
 

double TPrimer::deltaSValmax [private]
 

double TPrimer::deltaSValmin [private]
 

float TPrimer::evaluation [private]
 

The last quality evaluation.

int TPrimer::from
 

The beginning of the primer in a sequence.

double TPrimer::gaCount [private]
 

double TPrimer::gcCount [private]
 

double TPrimer::ggCount [private]
 

double TPrimer::gtCount [private]
 

double TPrimer::H [private]
 

double TPrimer::IUpairVals_max[3] [private]
 

double TPrimer::IUpairVals_min[3] [private]
 

wxString TPrimer::name [private]
 

float TPrimer::pgc [private]
 

GC%.

double TPrimer::S [private]
 

wxString TPrimer::sequence
 

The primer sequence.

double TPrimer::taCount [private]
 

float TPrimer::tm [private]
 

Melting temperature, nearest neighbour method.

float TPrimer::tm_gc [private]
 

Melting temperature, GC method.

float TPrimer::tm_salt [private]
 

Melting temperature, salt-adjusted.

int TPrimer::to
 

The end of a primer in the sequence.

bool TPrimer::upper
 

Upper (5'->3') or lower (3'->5') primer?


The documentation for this class was generated from the following files:
Generated on Fri Aug 11 16:19:48 2006 for GENtle by  doxygen 1.4.1