Package 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
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
-
-
Field Summary
Fields Modifier and Type Field Description protected FormattedOutput
format
int
numRates
number of rate categoriesdouble[]
probability
probability of each ratedouble[]
rate
rates of each rate category
-
Constructor Summary
Constructors Constructor Description RateDistribution(int n)
construct discrete distribution
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.Object
clone()
double[]
getCategoryProbabilities()
The non direct access methoddouble
getCategoryProbability(int category)
int
getNumberOfRates()
double
getRate(int category)
double[]
getRates()
protected void
printRates(java.io.PrintWriter out)
-
Methods inherited from class pal.misc.PalObjectListener.EventGenerator
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
-
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
-
-
-
-
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
-
-
Method Detail
-
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 classjava.lang.Object
-
-