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java.lang.Objectpal.substmodel.MultiRateMatrixHandler
public class MultiRateMatrixHandler
Constructor Summary | |
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MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices,
double[] equilibriumFrequencies,
double[] initialClassProportions)
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Method Summary | |
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MultiRateMatrixHandler |
getCopy()
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double |
getDefaultValue(int n)
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void |
getDefaultValues(double[] store,
int startIndex)
get default value parameter values |
double[] |
getEquilibriumFrequencies()
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double |
getLowerLimit(int n)
get lower parameter limit |
int |
getNumberOfParameters()
get number of parameters |
int |
getNumberOfSubstitutionClasses()
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void |
getParameters(double[] parameterStore,
int startIndex)
get model parameter |
double |
getSubstitutionClassDefaultValue()
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double |
getSubstitutionClassLowerLimit()
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double |
getSubstitutionClassUpperLimit()
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void |
getTransitionProbabilities(double distance,
double[][][] store)
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void |
getTransitionProbabilities(double distance,
int category,
double[][] store)
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void |
getTransitionProbabilitiesTranspose(double distance,
double[][][] store)
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void |
getTransitionProbabilitiesTranspose(double distance,
int category,
double[][] store)
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double |
getUpperLimit(int n)
get upper parameter limit |
void |
report(java.io.PrintWriter out)
Reporting stuff |
void |
setAllParameters(double[] rateParameters,
double[] classProportions)
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void |
setParameters(double[] parameters,
int startIndex)
set model parameter |
void |
setSubstitutionClassProbabilities(double[] classProportions)
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void |
setSubstitutionClassProbabilities(double[] classProportions,
int startIndex)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions)
Method Detail |
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public void setSubstitutionClassProbabilities(double[] classProportions)
public void setSubstitutionClassProbabilities(double[] classProportions, int startIndex)
public final int getNumberOfSubstitutionClasses()
public final MultiRateMatrixHandler getCopy()
public final double[] getEquilibriumFrequencies()
public void getTransitionProbabilities(double distance, double[][][] store)
public void getTransitionProbabilities(double distance, int category, double[][] store)
public void getTransitionProbabilitiesTranspose(double distance, double[][][] store)
public void getTransitionProbabilitiesTranspose(double distance, int category, double[][] store)
public void report(java.io.PrintWriter out)
out
- where to report toopublic final double getSubstitutionClassLowerLimit()
public final double getSubstitutionClassUpperLimit()
public final double getSubstitutionClassDefaultValue()
public double getLowerLimit(int n)
NeoParameterized
getLowerLimit
in interface NeoParameterized
n
- parameter number
public double getUpperLimit(int n)
NeoParameterized
getUpperLimit
in interface NeoParameterized
n
- parameter number
public double getDefaultValue(int n)
public int getNumberOfParameters()
NeoParameterized
getNumberOfParameters
in interface NeoParameterized
public void setAllParameters(double[] rateParameters, double[] classProportions)
public void setParameters(double[] parameters, int startIndex)
NeoParameterized
setParameters
in interface NeoParameterized
parameters
- the array holding the parametersstartIndex
- the index into the array that the related parameters start atpublic void getParameters(double[] parameterStore, int startIndex)
NeoParameterized
getParameters
in interface NeoParameterized
startIndex
- the index into the array that the related parameters start atpublic void getDefaultValues(double[] store, int startIndex)
NeoParameterized
getDefaultValues
in interface NeoParameterized
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