Package pal.substmodel
Class MultiRateMatrixHandler
- java.lang.Object
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- pal.substmodel.MultiRateMatrixHandler
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- All Implemented Interfaces:
java.io.Serializable
,NeoParameterized
public class MultiRateMatrixHandler extends java.lang.Object implements NeoParameterized, java.io.Serializable
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description MultiRateMatrixHandler
getCopy()
double
getDefaultValue(int n)
void
getDefaultValues(double[] store, int startIndex)
get default value parameter valuesdouble[]
getEquilibriumFrequencies()
double
getLowerLimit(int n)
get lower parameter limitint
getNumberOfParameters()
get number of parametersint
getNumberOfSubstitutionClasses()
void
getParameters(double[] parameterStore, int startIndex)
get model parameterdouble
getSubstitutionClassDefaultValue()
double
getSubstitutionClassLowerLimit()
double
getSubstitutionClassUpperLimit()
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(java.io.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 Detail
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MultiRateMatrixHandler
public MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions)
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Method Detail
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setSubstitutionClassProbabilities
public void setSubstitutionClassProbabilities(double[] classProportions)
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setSubstitutionClassProbabilities
public void setSubstitutionClassProbabilities(double[] classProportions, int startIndex)
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getNumberOfSubstitutionClasses
public final int getNumberOfSubstitutionClasses()
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getCopy
public final MultiRateMatrixHandler 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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getTransitionProbabilities
public void getTransitionProbabilities(double distance, int category, double[][] store)
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double distance, double[][][] store)
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double distance, int category, 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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getSubstitutionClassLowerLimit
public final double getSubstitutionClassLowerLimit()
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getSubstitutionClassUpperLimit
public final double getSubstitutionClassUpperLimit()
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getSubstitutionClassDefaultValue
public final double getSubstitutionClassDefaultValue()
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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)
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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)
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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
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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