Package pal.substmodel

Class RateDistribution

java.lang.Object
pal.misc.PalObjectListener.EventGenerator
pal.substmodel.RateDistribution
All Implemented Interfaces:
Serializable, Cloneable, Parameterized, Report
Direct Known Subclasses:
GammaRates, InvariableSites, UniformRate
public abstract class RateDistribution extends PalObjectListener.EventGenerator implements Parameterized, Report, Cloneable, Serializable
abstract base class for models of rate variation over sites employing a discrete rate distribution
Version:
$Id: RateDistribution.java,v 1.12 2004/05/19 04:05:21 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:

  • Field Details

    • numRates

      public int numRates
      number of rate categories

    • rate

      public double[] rate
      rates of each rate category

    • probability

      public double[] probability
      probability of each rate

    • format

      protected FormattedOutput format

  • Constructor Details

    • RateDistribution

      public RateDistribution(int n)
      construct discrete distribution
      Parameters:
      n - number of rate categories

  • Method Details

    • getNumberOfRates

      public final int getNumberOfRates()

    • getRates

      public final double[] getRates()

    • getRate

      public final double getRate(int category)

    • printRates

      protected void printRates(PrintWriter out)

    • getCategoryProbabilities

      public final double[] getCategoryProbabilities()
      The non direct access method

    • getCategoryProbability

      public final double getCategoryProbability(int category)

    • clone

      public Object clone()
      Overrides:
      clone in class Object