Package pal.substmodel
Class GeneralRateDistributionSubstitutionModel
java.lang.Object
pal.misc.PalObjectListener.EventGenerator
pal.misc.Parameterized.ParameterizedUser
pal.substmodel.GeneralRateDistributionSubstitutionModel
- All Implemented Interfaces:
Serializable
,Parameterized
,Report
,SubstitutionModel
public class GeneralRateDistributionSubstitutionModel
extends Parameterized.ParameterizedUser
implements SubstitutionModel
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
Nested classes/interfaces inherited from interface pal.substmodel.SubstitutionModel
SubstitutionModel.Utils
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Constructor Summary
ConstructorsConstructorDescriptionGeneralRateDistributionSubstitutionModel
(NeoRateMatrix base, RateDistribution rateDistribution, DataType dt, double[] frequencies) -
Method Summary
Modifier and TypeMethodDescriptionvoid
clone()
getCopy()
double[]
Should return a double[] array of the related equilibrium frequencies.double[]
int
May return nulldouble[]
double[]
double
getTransitionCategoryProbability
(int category) 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
void
report
(PrintWriter out) print human readable report (e.g., on parameters and associated model)toString()
Methods inherited from class pal.misc.Parameterized.ParameterizedUser
getAllParameters, getDefaultValue, getLowerLimit, getNumParameters, getParameter, getRandomParameterValue, getUpperLimit, randomiseParameters, setParameter, setParameterizedBase, setParameterSE
Methods inherited from class pal.misc.PalObjectListener.EventGenerator
fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
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Constructor Details
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GeneralRateDistributionSubstitutionModel
public GeneralRateDistributionSubstitutionModel(NeoRateMatrix base, RateDistribution rateDistribution, DataType dt, double[] frequencies)
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Method Details
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getMatrixParameters
public double[] getMatrixParameters() -
getRateDistributionParameters
public double[] getRateDistributionParameters() -
getDataType
- Specified by:
getDataType
in interfaceSubstitutionModel
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getNumberOfTransitionCategories
public int getNumberOfTransitionCategories()- Specified by:
getNumberOfTransitionCategories
in interfaceSubstitutionModel
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getTransitionCategoryProbability
public double getTransitionCategoryProbability(int category) - Specified by:
getTransitionCategoryProbability
in interfaceSubstitutionModel
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getTransitionCategoryProbabilities
public double[] getTransitionCategoryProbabilities()- Specified by:
getTransitionCategoryProbabilities
in interfaceSubstitutionModel
- Returns:
- all the category probabilites for each category respectively.
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getEquilibriumFrequencies
public double[] getEquilibriumFrequencies()Description copied from interface:SubstitutionModel
Should return a double[] array of the related equilibrium frequencies. As a rule, callers should not alter the returned array (it may be used internally)- Specified by:
getEquilibriumFrequencies
in interfaceSubstitutionModel
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getTransitionProbabilities
public void getTransitionProbabilities(double branchLength, double[][][] store) Description copied from interface:SubstitutionModel
Table is organized as [transition_group][from][to]- Specified by:
getTransitionProbabilities
in interfaceSubstitutionModel
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getTransitionProbabilities
public void getTransitionProbabilities(double branchLength, int category, double[][] store) Description copied from interface:SubstitutionModel
Table is organized as [transition_group][from][to]- Specified by:
getTransitionProbabilities
in interfaceSubstitutionModel
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] store) Description copied from interface:SubstitutionModel
Table is organized as [transition_group][to][from]- Specified by:
getTransitionProbabilitiesTranspose
in interfaceSubstitutionModel
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] store) Description copied from interface:SubstitutionModel
Table is organized as [transition_group][to][from]- Specified by:
getTransitionProbabilitiesTranspose
in interfaceSubstitutionModel
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addPalObjectListener
- Specified by:
addPalObjectListener
in interfaceSubstitutionModel
- Overrides:
addPalObjectListener
in classPalObjectListener.EventGenerator
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removePalObjectListener
- Specified by:
removePalObjectListener
in interfaceSubstitutionModel
- Overrides:
removePalObjectListener
in classPalObjectListener.EventGenerator
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getOrthogonalHints
Description copied from interface:SubstitutionModel
May return null- Specified by:
getOrthogonalHints
in interfaceSubstitutionModel
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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model) -
toString
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clone
- Specified by:
clone
in interfaceSubstitutionModel
- Overrides:
clone
in classObject
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getCopy
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