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java.lang.Objectpal.substmodel.RateMatrixHandler
public class RateMatrixHandler
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Constructor Summary | |
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RateMatrixHandler(NeoRateMatrix rateMatrix,
double[] equilibriumFrequencies)
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Method Summary | |
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RateMatrixHandler |
getCopy()
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double |
getDefaultValue(int n)
get default value of parameter |
double[] |
getEquilibriumFrequencies()
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double |
getLowerLimit(int n)
get lower parameter limit |
int |
getNumParameters()
get number of parameters |
double |
getParameter(int n)
get model parameter |
void |
getTransitionProbabilities(double distance,
double[][] store)
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void |
getTransitionProbabilitiesTranspose(double distance,
double[][] store)
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double |
getUpperLimit(int n)
get upper parameter limit |
void |
report(java.io.PrintWriter out)
Reporting stuff |
void |
setParameter(double param,
int n)
set model parameter |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
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 RateMatrixHandler(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies)
Method Detail |
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public final RateMatrixHandler getCopy()
public final double[] getEquilibriumFrequencies()
public void getTransitionProbabilities(double distance, double[][] store)
public void getTransitionProbabilitiesTranspose(double distance, double[][] store)
public void report(java.io.PrintWriter out)
out
- where to report toopublic int getNumParameters()
Parameterized
getNumParameters
in interface Parameterized
public void setParameter(double param, int n)
Parameterized
setParameter
in interface Parameterized
param
- parameter valuen
- parameter numberpublic double getParameter(int n)
Parameterized
getParameter
in interface Parameterized
n
- parameter number
public void setParameterSE(double paramSE, int n)
Parameterized
setParameterSE
in interface Parameterized
paramSE
- standard error of parameter valuen
- parameter numberpublic double getLowerLimit(int n)
Parameterized
getLowerLimit
in interface Parameterized
n
- parameter number
public double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter number
public double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter number
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