Package pal.substmodel
Class SimpleRateMatrixGroup
- java.lang.Object
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- pal.substmodel.SimpleRateMatrixGroup
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- All Implemented Interfaces:
java.io.Serializable
,RateMatrixGroup
public abstract class SimpleRateMatrixGroup extends java.lang.Object implements RateMatrixGroup
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices, double[] equilibriumFrequencies, double[] initialClassProbabilities, DataType dataType)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description DataType
getDataType()
double
getDefaultValue(int n)
double[]
getEquilibriumFrequencies()
double
getLowerLimit(int n)
int
getNumberOfParameters()
int
getNumberOfTransitionCategories()
java.lang.String
getSummary(double[] parameters, double[] categoryProbabilities)
void
getTransitionProbabilities(double branchLength, double[][][] tableStore)
void
getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
void
getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
void
getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
double
getUpperLimit(int n)
void
setParameters(double[] parameters, double[] categoryProbabilities)
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface pal.substmodel.RateMatrixGroup
getSummary, updateParameters
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Constructor Detail
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SimpleRateMatrixGroup
public SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices, double[] equilibriumFrequencies, double[] initialClassProbabilities, DataType dataType)
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Method Detail
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getNumberOfParameters
public int getNumberOfParameters()
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getLowerLimit
public double getLowerLimit(int n)
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getUpperLimit
public double getUpperLimit(int n)
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getDefaultValue
public double getDefaultValue(int n)
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setParameters
public void setParameters(double[] parameters, double[] categoryProbabilities)
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getEquilibriumFrequencies
public double[] getEquilibriumFrequencies()
- Specified by:
getEquilibriumFrequencies
in interfaceRateMatrixGroup
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getDataType
public DataType getDataType()
- Specified by:
getDataType
in interfaceRateMatrixGroup
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getNumberOfTransitionCategories
public int getNumberOfTransitionCategories()
- Specified by:
getNumberOfTransitionCategories
in interfaceRateMatrixGroup
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getTransitionProbabilities
public void getTransitionProbabilities(double branchLength, double[][][] tableStore)
- Specified by:
getTransitionProbabilities
in interfaceRateMatrixGroup
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
- Specified by:
getTransitionProbabilitiesTranspose
in interfaceRateMatrixGroup
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getTransitionProbabilities
public void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
- Specified by:
getTransitionProbabilities
in interfaceRateMatrixGroup
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
- Specified by:
getTransitionProbabilitiesTranspose
in interfaceRateMatrixGroup
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getSummary
public java.lang.String getSummary(double[] parameters, double[] categoryProbabilities)
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