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java.lang.Objectpal.misc.PalObjectListener.EventGenerator
pal.substmodel.RateDistribution
pal.substmodel.InvariableSites
public class InvariableSites
invariable sites model (two-rate model with mean rate = 1.0)
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Field Summary |
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Fields inherited from class pal.substmodel.RateDistribution |
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format, numRates, probability, rate |
Constructor Summary | |
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InvariableSites(double f)
construct discrete rate distribution with two rates (one invariable and one variable) |
Method Summary | |
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double |
getDefaultValue(int n)
get default value of parameter |
double |
getLowerLimit(int n)
get lower parameter limit |
int |
getNumParameters()
get number of parameters |
double |
getParameter(int n)
get model parameter |
double |
getUpperLimit(int n)
get upper parameter limit |
boolean |
isDistributionIndependentlyMutable()
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void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
void |
setParameter(double param,
int n)
set model parameter |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
Methods inherited from class pal.substmodel.RateDistribution |
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clone, getCategoryProbabilities, getCategoryProbability, getNumberOfRates, getRate, getRates, printRates |
Methods inherited from class pal.misc.PalObjectListener.EventGenerator |
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addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public InvariableSites(double f)
f
- fraction of invariable sitesMethod Detail |
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public void report(java.io.PrintWriter out)
Report
report
in interface Report
out
- output streampublic 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 number
public 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 number
public double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter number
public double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter number
public boolean isDistributionIndependentlyMutable()
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