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java.lang.Objectpal.misc.PalObjectListener.EventGenerator
pal.misc.Parameterized.ParameterizedUser
pal.substmodel.GeneralRateDistributionSubstitutionModel
public class GeneralRateDistributionSubstitutionModel
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel |
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SubstitutionModel.Utils |
Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser |
Constructor Summary | |
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GeneralRateDistributionSubstitutionModel(NeoRateMatrix base,
RateDistribution rateDistribution,
DataType dt,
double[] frequencies)
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Method Summary | |
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void |
addPalObjectListener(PalObjectListener l)
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java.lang.Object |
clone()
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SubstitutionModel |
getCopy()
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DataType |
getDataType()
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double[] |
getEquilibriumFrequencies()
Should return a double[] array of the related equilibrium frequencies. |
double[] |
getMatrixParameters()
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int |
getNumberOfTransitionCategories()
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OrthogonalHints |
getOrthogonalHints()
May return null |
double[] |
getRateDistributionParameters()
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double[] |
getTransitionCategoryProbabilities()
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double |
getTransitionCategoryProbability(int category)
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void |
getTransitionProbabilities(double branchLength,
double[][][] store)
Table is organized as [transition_group][from][to] |
void |
getTransitionProbabilities(double branchLength,
int category,
double[][] store)
Table is organized as [transition_group][from][to] |
void |
getTransitionProbabilitiesTranspose(double branchLength,
double[][][] store)
Table is organized as [transition_group][to][from] |
void |
getTransitionProbabilitiesTranspose(double branchLength,
int category,
double[][] store)
Table is organized as [transition_group][to][from] |
void |
removePalObjectListener(PalObjectListener l)
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void |
report(java.io.PrintWriter out)
print human readable report (e.g., on parameters and associated model) |
java.lang.String |
toString()
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Methods inherited from class pal.misc.Parameterized.ParameterizedUser |
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getAllParameters, getDefaultValue, getLowerLimit, getNumParameters, getParameter, getRandomParameterValue, getUpperLimit, randomiseParameters, setParameter, setParameterizedBase, setParameterSE |
Methods inherited from class pal.misc.PalObjectListener.EventGenerator |
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fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface pal.misc.Parameterized |
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getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE |
Constructor Detail |
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public GeneralRateDistributionSubstitutionModel(NeoRateMatrix base, RateDistribution rateDistribution, DataType dt, double[] frequencies)
Method Detail |
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public double[] getMatrixParameters()
public double[] getRateDistributionParameters()
public DataType getDataType()
getDataType
in interface SubstitutionModel
public int getNumberOfTransitionCategories()
getNumberOfTransitionCategories
in interface SubstitutionModel
public double getTransitionCategoryProbability(int category)
getTransitionCategoryProbability
in interface SubstitutionModel
public double[] getTransitionCategoryProbabilities()
getTransitionCategoryProbabilities
in interface SubstitutionModel
public double[] getEquilibriumFrequencies()
SubstitutionModel
getEquilibriumFrequencies
in interface SubstitutionModel
public void getTransitionProbabilities(double branchLength, double[][][] store)
SubstitutionModel
getTransitionProbabilities
in interface SubstitutionModel
public void getTransitionProbabilities(double branchLength, int category, double[][] store)
SubstitutionModel
getTransitionProbabilities
in interface SubstitutionModel
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] store)
SubstitutionModel
getTransitionProbabilitiesTranspose
in interface SubstitutionModel
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] store)
SubstitutionModel
getTransitionProbabilitiesTranspose
in interface SubstitutionModel
public void addPalObjectListener(PalObjectListener l)
addPalObjectListener
in interface SubstitutionModel
addPalObjectListener
in class PalObjectListener.EventGenerator
public void removePalObjectListener(PalObjectListener l)
removePalObjectListener
in interface SubstitutionModel
removePalObjectListener
in class PalObjectListener.EventGenerator
public OrthogonalHints getOrthogonalHints()
SubstitutionModel
getOrthogonalHints
in interface SubstitutionModel
public void report(java.io.PrintWriter out)
Report
report
in interface Report
out
- output streampublic java.lang.String toString()
toString
in class java.lang.Object
public java.lang.Object clone()
clone
in interface SubstitutionModel
clone
in class java.lang.Object
public SubstitutionModel getCopy()
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