BaseCount Class Reference

#include <motif.hh>

Public Member Functions
	BaseCount (int a, int c, int g, int t)
	BaseCount (const char *sequence, int len=-1)
void	normalize ()
void	addSequence (const char *sequence, int len)
void	addCharacter (char nucleotide, bool subtract=false)
void	reverse ()

Static Public Member Functions
static void	init ()
static int	weight (BaseCount bc1, BaseCount bc2)
static double	doubleWeight (BaseCount bc1, BaseCount bc2)
static int	gcContentWeight (BaseCount bc1, BaseCount bc2)
static int	gcContentClass (double gcContent)
static int	gcContentClassWeight (BaseCount bc1, BaseCount bc2)
static double	multiNormalKernelWeight (BaseCount bc1, BaseCount bc2)
static void	setWeightMatrix (string matrixFileName)
static double	phi (double x, double sigma)

Public Attributes
int	a
int	c
int	g
int	t
double	ra
double	rc
double	rg
double	rt

Static Public Attributes
static WeighingType	weithType = equalWeights
static Matrix< double >	weighingMatrix = 0

Detailed Description

Author

Mario Stanke

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

• include/motif.hh
• src/motif.cc