java.io.Serializable
, java.lang.Cloneable
, Parameterized
, Report
GammaRates
, InvariableSites
, UniformRate
public abstract class RateDistribution extends PalObjectListener.EventGenerator implements Parameterized, Report, java.lang.Cloneable, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Modifier and Type | Field | Description |
---|---|---|
protected FormattedOutput |
format |
|
int |
numRates |
number of rate categories
|
double[] |
probability |
probability of each rate
|
double[] |
rate |
rates of each rate category
|
Constructor | Description |
---|---|
RateDistribution(int n) |
construct discrete distribution
|
Modifier and Type | Method | Description |
---|---|---|
java.lang.Object |
clone() |
|
double[] |
getCategoryProbabilities() |
The non direct access method
|
double |
getCategoryProbability(int category) |
|
int |
getNumberOfRates() |
|
double |
getRate(int category) |
|
double[] |
getRates() |
|
protected void |
printRates(java.io.PrintWriter out) |
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
public int numRates
public double[] rate
public double[] probability
protected FormattedOutput format
public RateDistribution(int n)
n
- number of rate categoriespublic final int getNumberOfRates()
public final double[] getRates()
public final double getRate(int category)
protected void printRates(java.io.PrintWriter out)
public final double[] getCategoryProbabilities()
public final double getCategoryProbability(int category)
public java.lang.Object clone()
clone
in class java.lang.Object