pal.substmodel
public class RateMatrixHandler extends java.lang.Object implements Parameterized, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
Constructor and Description |
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RateMatrixHandler(NeoRateMatrix rateMatrix,
double[] equilibriumFrequencies) |
Modifier and Type | Method and Description |
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RateMatrixHandler |
getCopy() |
double |
getDefaultValue(int n)
get default value of parameter
|
double[] |
getEquilibriumFrequencies() |
double |
getLowerLimit(int n)
get lower parameter limit
|
int |
getNumParameters()
get number of parameters
|
double |
getParameter(int n)
get model parameter
|
void |
getTransitionProbabilities(double distance,
double[][] store) |
void |
getTransitionProbabilitiesTranspose(double distance,
double[][] store) |
double |
getUpperLimit(int n)
get upper parameter limit
|
void |
report(java.io.PrintWriter out)
Reporting stuff
|
void |
setParameter(double param,
int n)
set model parameter
|
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter
|
public RateMatrixHandler(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies)
public final RateMatrixHandler getCopy()
public final double[] getEquilibriumFrequencies()
public void getTransitionProbabilities(double distance, double[][] store)
public void getTransitionProbabilitiesTranspose(double distance, double[][] store)
public void report(java.io.PrintWriter out)
out
- where to report toopublic 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 number