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SUMMARY: INNER | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object | +--pal.substmodel.RateDistribution | +--pal.substmodel.InvariableSites
invariable sites model (two-rate model with mean rate = 1.0)
Fields inherited from class pal.substmodel.RateDistribution |
format, numRates, probability, rate |
Constructor Summary | |
InvariableSites(double f)
construct discrete rate distribution with two rates (one invariable and one variable) |
Method Summary | |
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 |
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 |
clone, printRates |
Methods inherited from class java.lang.Object |
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public InvariableSites(double f)
f
- fraction of invariable sitesMethod Detail |
public void report(java.io.PrintWriter out)
Report
pal.misc.Report
out
- output streampublic int getNumParameters()
Parameterized
pal.misc.Parameterized
public void setParameter(double param, int n)
Parameterized
pal.misc.Parameterized
param
- parameter valuen
- parameter numberpublic double getParameter(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic void setParameterSE(double paramSE, int n)
Parameterized
pal.misc.Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getUpperLimit(int n)
Parameterized
pal.misc.Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
pal.misc.Parameterized
n
- parameter number
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