Package pal.substmodel
Class MultiRateMatrixHandler
java.lang.Object
pal.substmodel.MultiRateMatrixHandler
- All Implemented Interfaces:
Serializable
,NeoParameterized
- See Also:
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Constructor Summary
ConstructorsConstructorDescriptionMultiRateMatrixHandler
(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions) -
Method Summary
Modifier and TypeMethodDescriptionfinal MultiRateMatrixHandler
getCopy()
double
getDefaultValue
(int n) void
getDefaultValues
(double[] store, int startIndex) get default value parameter valuesfinal double[]
double
getLowerLimit
(int n) get lower parameter limitint
get number of parametersfinal int
void
getParameters
(double[] parameterStore, int startIndex) get model parameterfinal double
final double
final double
void
getTransitionProbabilities
(double distance, double[][][] store) void
getTransitionProbabilities
(double distance, int category, double[][] store) void
getTransitionProbabilitiesTranspose
(double distance, double[][][] store) void
getTransitionProbabilitiesTranspose
(double distance, int category, double[][] store) double
getUpperLimit
(int n) get upper parameter limitvoid
report
(PrintWriter out) Reporting stuffvoid
setAllParameters
(double[] rateParameters, double[] classProportions) void
setParameters
(double[] parameters, int startIndex) set model parametervoid
setSubstitutionClassProbabilities
(double[] classProportions) void
setSubstitutionClassProbabilities
(double[] classProportions, int startIndex)
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Constructor Details
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MultiRateMatrixHandler
public MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions)
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Method Details
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setSubstitutionClassProbabilities
public void setSubstitutionClassProbabilities(double[] classProportions) -
setSubstitutionClassProbabilities
public void setSubstitutionClassProbabilities(double[] classProportions, int startIndex) -
getNumberOfSubstitutionClasses
public final int getNumberOfSubstitutionClasses() -
getCopy
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getEquilibriumFrequencies
public final double[] getEquilibriumFrequencies() -
getTransitionProbabilities
public void getTransitionProbabilities(double distance, double[][][] store) -
getTransitionProbabilities
public void getTransitionProbabilities(double distance, int category, double[][] store) -
getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double distance, double[][][] store) -
getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double distance, int category, double[][] store) -
report
Reporting stuff- Parameters:
out
- where to report too
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getSubstitutionClassLowerLimit
public final double getSubstitutionClassLowerLimit() -
getSubstitutionClassUpperLimit
public final double getSubstitutionClassUpperLimit() -
getSubstitutionClassDefaultValue
public final double getSubstitutionClassDefaultValue() -
getLowerLimit
public double getLowerLimit(int n) Description copied from interface:NeoParameterized
get lower parameter limit- Specified by:
getLowerLimit
in interfaceNeoParameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
public double getUpperLimit(int n) Description copied from interface:NeoParameterized
get upper parameter limit- Specified by:
getUpperLimit
in interfaceNeoParameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValue
public double getDefaultValue(int n) -
getNumberOfParameters
public int getNumberOfParameters()Description copied from interface:NeoParameterized
get number of parameters- Specified by:
getNumberOfParameters
in interfaceNeoParameterized
- Returns:
- number of parameters
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setAllParameters
public void setAllParameters(double[] rateParameters, double[] classProportions) -
setParameters
public void setParameters(double[] parameters, int startIndex) Description copied from interface:NeoParameterized
set model parameter- Specified by:
setParameters
in interfaceNeoParameterized
- Parameters:
parameters
- the array holding the parametersstartIndex
- the index into the array that the related parameters start at
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getParameters
public void getParameters(double[] parameterStore, int startIndex) Description copied from interface:NeoParameterized
get model parameter- Specified by:
getParameters
in interfaceNeoParameterized
- Parameters:
startIndex
- the index into the array that the related parameters start at
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getDefaultValues
public void getDefaultValues(double[] store, int startIndex) Description copied from interface:NeoParameterized
get default value parameter values- Specified by:
getDefaultValues
in interfaceNeoParameterized
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