public class InvariableSites extends RateDistribution implements java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
format, numRates, probability, rate
Constructor and Description |
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InvariableSites(double f)
construct discrete rate distribution with two rates
(one invariable and one variable)
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Modifier and Type | Method and Description |
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double |
getDefaultValue(int n)
get default value of parameter
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double |
getLowerLimit(int n)
get lower parameter limit
|
int |
getNumParameters()
get number of parameters
|
double |
getParameter(int n)
get model parameter
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double |
getUpperLimit(int n)
get upper parameter limit
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boolean |
isDistributionIndependentlyMutable() |
void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model)
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void |
setParameter(double param,
int n)
set model parameter
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void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter
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clone, getCategoryProbabilities, getCategoryProbability, getNumberOfRates, getRate, getRates, printRates
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
public InvariableSites(double f)
f
- fraction of invariable sitespublic void report(java.io.PrintWriter out)
Report
public int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public void setParameter(double param, int n)
Parameterized
setParameter
in interface Parameterized
param
- parameter valuen
- parameter numberpublic double getParameter(int n)
Parameterized
getParameter
in interface Parameterized
n
- parameter numberpublic void setParameterSE(double paramSE, int n)
Parameterized
setParameterSE
in interface Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
getLowerLimit
in interface Parameterized
n
- parameter numberpublic double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter numberpublic boolean isDistributionIndependentlyMutable()