Class 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