pal.substmodel
Class RateDistribution

java.lang.Object
  |
  +--pal.substmodel.RateDistribution
All Implemented Interfaces:
java.lang.Cloneable, Parameterized, Report, java.io.Serializable
Direct Known Subclasses:
GammaRates, InvariableSites, UniformRate

public abstract class RateDistribution
extends java.lang.Object
implements Parameterized, Report, java.lang.Cloneable, java.io.Serializable

abstract base class for models of rate variation over sites employing a discrete rate distribution

See Also:
Serialized Form

Field Summary
protected  FormattedOutput format
           
 int numRates
          number of rate categories
 double[] probability
          probability of each rate
 double[] rate
          rates of each rate category
 
Constructor Summary
RateDistribution(int n)
          construct discrete distribution
 
Method Summary
 java.lang.Object clone()
           
protected  void printRates(java.io.PrintWriter out)
           
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
 
Methods inherited from interface pal.misc.Report
report
 

Field Detail

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 Detail

RateDistribution

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

printRates

protected void printRates(java.io.PrintWriter out)

clone

public java.lang.Object clone()
Overrides:
clone in class java.lang.Object