Package pal.substmodel
Class RateMatrixHandler
- java.lang.Object
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- pal.substmodel.RateMatrixHandler
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- All Implemented Interfaces:
java.io.Serializable
,Parameterized
public class RateMatrixHandler extends java.lang.Object implements Parameterized, java.io.Serializable
- See Also:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Constructor Summary
Constructors Constructor Description RateMatrixHandler(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description RateMatrixHandler
getCopy()
double
getDefaultValue(int n)
get default value of parameterdouble[]
getEquilibriumFrequencies()
double
getLowerLimit(int n)
get lower parameter limitint
getNumParameters()
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(java.io.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 Detail
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RateMatrixHandler
public RateMatrixHandler(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies)
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Method Detail
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getCopy
public final RateMatrixHandler getCopy()
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getEquilibriumFrequencies
public final double[] getEquilibriumFrequencies()
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getTransitionProbabilities
public void getTransitionProbabilities(double distance, double[][] store)
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double distance, double[][] store)
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report
public void report(java.io.PrintWriter out)
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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