org.jscience.biology.genetics
Class GeneticsUtils

java.lang.Object
  extended by org.jscience.biology.genetics.GeneticsUtils

public final class GeneticsUtils
extends java.lang.Object

A class representing some useful methods for population genetics.


Constructor Summary
GeneticsUtils()
           
 
Method Summary
static double getAlleleFrequencyVariance(double p, double N)
          DOCUMENT ME!
static double getEffectivePopulationSize(double[] populationSizes)
          DOCUMENT ME!
static double getEffectivePopulationSize(double Nm, double Nf)
          DOCUMENT ME!
static double getEwenSampling(int omega, DoubleVector vector)
          The Ewens's sampling formula, see http://en.wikipedia.org/wiki/Ewens%27s_sampling_formula omega must be positive although this is unchecked Elements of the vector must be non negative numbers although this is unchecked
static double getGenotypeFrequency(double[] genotypeKey, double[] allelesfrequencies)
          DOCUMENT ME!
static double getInbreedingEffictiveSize(double ft1)
          DOCUMENT ME!
static double getInbreedingEffictiveSize(double ft, double ft1)
          DOCUMENT ME!
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GeneticsUtils

public GeneticsUtils()
Method Detail

getEwenSampling

public static final double getEwenSampling(int omega,
                                           DoubleVector vector)
The Ewens's sampling formula, see http://en.wikipedia.org/wiki/Ewens%27s_sampling_formula omega must be positive although this is unchecked Elements of the vector must be non negative numbers although this is unchecked

Parameters:
omega - DOCUMENT ME!
vector - DOCUMENT ME!
Returns:
DOCUMENT ME!

getAlleleFrequencyVariance

public static final double getAlleleFrequencyVariance(double p,
                                                      double N)
DOCUMENT ME!

Parameters:
p - DOCUMENT ME!
N - DOCUMENT ME!
Returns:
DOCUMENT ME!

getInbreedingEffictiveSize

public static final double getInbreedingEffictiveSize(double ft,
                                                      double ft1)
DOCUMENT ME!

Parameters:
ft - DOCUMENT ME!
ft1 - DOCUMENT ME!
Returns:
DOCUMENT ME!

getInbreedingEffictiveSize

public static final double getInbreedingEffictiveSize(double ft1)
DOCUMENT ME!

Parameters:
ft1 - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEffectivePopulationSize

public static final double getEffectivePopulationSize(double[] populationSizes)
DOCUMENT ME!

Parameters:
populationSizes - DOCUMENT ME!
Returns:
DOCUMENT ME!

getEffectivePopulationSize

public static final double getEffectivePopulationSize(double Nm,
                                                      double Nf)
DOCUMENT ME!

Parameters:
Nm - DOCUMENT ME!
Nf - DOCUMENT ME!
Returns:
DOCUMENT ME!

getGenotypeFrequency

public static final double getGenotypeFrequency(double[] genotypeKey,
                                                double[] allelesfrequencies)
DOCUMENT ME!

Parameters:
genotypeKey - DOCUMENT ME!
allelesfrequencies - DOCUMENT ME!
Returns:
DOCUMENT ME!