Package pal.substmodel
Class RateMatrixHandler
java.lang.Object
pal.substmodel.RateMatrixHandler
- All Implemented Interfaces:
Serializable
,Parameterized
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Constructor Summary
ConstructorsConstructorDescriptionRateMatrixHandler
(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies) -
Method Summary
Modifier and TypeMethodDescriptionfinal RateMatrixHandler
getCopy()
double
getDefaultValue
(int n) get default value of parameterfinal double[]
double
getLowerLimit
(int n) get lower parameter limitint
get number of parametersdouble
getParameter
(int n) get model parametervoid
getTransitionProbabilities
(double distance, double[][] store) void
getTransitionProbabilitiesTranspose
(double distance, double[][] store) double
getUpperLimit
(int n) get upper parameter limitvoid
report
(PrintWriter out) Reporting stuffvoid
setParameter
(double param, int n) set model parametervoid
setParameterSE
(double paramSE, int n) set standard errors for model parameter
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Constructor Details
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RateMatrixHandler
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Method Details
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getCopy
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getEquilibriumFrequencies
public final double[] getEquilibriumFrequencies() -
getTransitionProbabilities
public void getTransitionProbabilities(double distance, double[][] store) -
getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double distance, double[][] store) -
report
Reporting stuff- Parameters:
out
- where to report too
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getNumParameters
public int getNumParameters()Description copied from interface:Parameterized
get number of parameters- Specified by:
getNumParameters
in interfaceParameterized
- Returns:
- number of parameters
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setParameter
public void setParameter(double param, int n) Description copied from interface:Parameterized
set model parameter- Specified by:
setParameter
in interfaceParameterized
- Parameters:
param
- parameter valuen
- parameter number
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getParameter
public double getParameter(int n) Description copied from interface:Parameterized
get model parameter- Specified by:
getParameter
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- parameter value
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setParameterSE
public void setParameterSE(double paramSE, int n) Description copied from interface:Parameterized
set standard errors for model parameter- Specified by:
setParameterSE
in interfaceParameterized
- Parameters:
paramSE
- standard error of parameter valuen
- parameter number
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getLowerLimit
public double getLowerLimit(int n) Description copied from interface:Parameterized
get lower parameter limit- Specified by:
getLowerLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
public double getUpperLimit(int n) Description copied from interface:Parameterized
get upper parameter limit- Specified by:
getUpperLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValue
public double getDefaultValue(int n) Description copied from interface:Parameterized
get default value of parameter- Specified by:
getDefaultValue
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- default value
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