pal.substmodel
Class RateDistribution
java.lang.Object
pal.misc.PalObjectListener.EventGenerator
pal.substmodel.RateDistribution
- All Implemented Interfaces:
- java.io.Serializable, java.lang.Cloneable, Parameterized, Report
- Direct Known Subclasses:
- GammaRates, InvariableSites, UniformRate
public abstract class RateDistribution
- extends PalObjectListener.EventGenerator
- implements Parameterized, Report, java.lang.Cloneable, java.io.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:
- Serialized Form
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
RateDistribution
public RateDistribution(int n)
- construct discrete distribution
- Parameters:
n
- number of rate categories
getNumberOfRates
public final int getNumberOfRates()
getRates
public final double[] getRates()
getRate
public final double getRate(int category)
printRates
protected void printRates(java.io.PrintWriter out)
getCategoryProbabilities
public final double[] getCategoryProbabilities()
- The non direct access method
getCategoryProbability
public final double getCategoryProbability(int category)
clone
public java.lang.Object clone()
- Overrides:
clone
in class java.lang.Object