Package pal.substmodel
Class YangCodonModel.SimplePositiveSelection
java.lang.Object
pal.misc.PalObjectListener.EventGenerator
pal.substmodel.YangCodonModel.SimplePositiveSelection
- All Implemented Interfaces:
Serializable
,Parameterized
,Report
,SubstitutionModel
- Enclosing class:
- YangCodonModel
public static class YangCodonModel.SimplePositiveSelection
extends PalObjectListener.EventGenerator
implements SubstitutionModel
A Substitution Model which can be used to implment the Postitive Selection (with out continuous rate stuff)
Codon model of [1] which uses the weighted sum of a three base Codon model where
omega=0, omega=1 and omega=free
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. Genetics 148: 929-936.
[1] Nielsen, R., Yang Z., 1998 Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene. Genetics 148: 929-936.
- 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
ConstructorsModifierConstructorDescriptionSimplePositiveSelection
(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega) SimplePositiveSelection
(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1) SimplePositiveSelection
(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1, double p2) protected
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Method Summary
Modifier and TypeMethodDescriptionclone()
getCopy()
double
getDefaultValue
(int n) get default value of parameterdouble[]
Should return a double[] array of the related equilibrium frequencies.double
getLowerLimit
(int n) get lower parameter limitint
int
Five parameters, three proportions, kappa, omega.May return nulldouble
getParameter
(int n) get model parameterdouble[]
double
getTransitionCategoryProbability
(int category) void
getTransitionProbabilities
(double branchLength, double[][][] tableStore) Table is organized as [transition_group][from][to]void
getTransitionProbabilities
(double branchLength, int category, double[][] tableStore) Table is organized as [tree_group][from][to]void
getTransitionProbabilitiesTranspose
(double branchLength, double[][][] tableStore) Table is organized as [tree_group][to][from]void
getTransitionProbabilitiesTranspose
(double branchLength, int category, double[][] tableStore) Table is organized as [to][from]double
getUpperLimit
(int n) get upper parameter limitvoid
report
(PrintWriter pw) print human readable report (e.g., on parameters and associated model)void
setParameter
(double param, int n) set model parametervoid
setParameterSE
(double paramSE, int n) set standard errors for model parameterfinal void
setTransitionCategoryProbabilities
(double p0, double p1, double p2) We use three parameters instead of two to make opimisation easier (there are effectively only *two* parameters though)toString()
Methods inherited from class pal.misc.PalObjectListener.EventGenerator
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface pal.substmodel.SubstitutionModel
addPalObjectListener, removePalObjectListener
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Constructor Details
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SimplePositiveSelection
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SimplePositiveSelection
public SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega) -
SimplePositiveSelection
public SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1) -
SimplePositiveSelection
public SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1, double p2)
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Method Details
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clone
- Specified by:
clone
in interfaceSubstitutionModel
- Overrides:
clone
in classObject
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getCopy
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getDataType
- Specified by:
getDataType
in interfaceSubstitutionModel
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getNumberOfTransitionCategories
public int getNumberOfTransitionCategories()- Specified by:
getNumberOfTransitionCategories
in interfaceSubstitutionModel
- Returns:
- 3
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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[][][] tableStore) 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[][] tableStore) Table is organized as [tree_group][from][to]- Specified by:
getTransitionProbabilities
in interfaceSubstitutionModel
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore) Table is organized as [tree_group][to][from]- Specified by:
getTransitionProbabilitiesTranspose
in interfaceSubstitutionModel
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getTransitionProbabilitiesTranspose
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore) Table is organized as [to][from]- Specified by:
getTransitionProbabilitiesTranspose
in interfaceSubstitutionModel
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setTransitionCategoryProbabilities
public final void setTransitionCategoryProbabilities(double p0, double p1, double p2) We use three parameters instead of two to make opimisation easier (there are effectively only *two* parameters though)- Parameters:
p0
-p1
-p2
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getNumParameters
public int getNumParameters()Five parameters, three proportions, kappa, omega. Even though the probabilities could be represented by two parameters we use three for ease of optimisation- Specified by:
getNumParameters
in interfaceParameterized
- Returns:
- number of parameters
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setParameter
public void setParameter(double param, int n) Description copied from interface:Parameterized
set model parameter- Specified by:
setParameter
in interfaceParameterized
- Parameters:
param
- parameter valuen
- parameter number
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getParameter
public double getParameter(int n) Description copied from interface:Parameterized
get model parameter- Specified by:
getParameter
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- parameter value
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setParameterSE
public void setParameterSE(double paramSE, int n) Description copied from interface:Parameterized
set standard errors for model parameter- Specified by:
setParameterSE
in interfaceParameterized
- Parameters:
paramSE
- standard error of parameter valuen
- parameter number
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getLowerLimit
public double getLowerLimit(int n) Description copied from interface:Parameterized
get lower parameter limit- Specified by:
getLowerLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
public double getUpperLimit(int n) Description copied from interface:Parameterized
get upper parameter limit- Specified by:
getUpperLimit
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValue
public double getDefaultValue(int n) Description copied from interface:Parameterized
get default value of parameter- Specified by:
getDefaultValue
in interfaceParameterized
- Parameters:
n
- parameter number- Returns:
- default value
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getOrthogonalHints
Description copied from interface:SubstitutionModel
May return null- Specified by:
getOrthogonalHints
in interfaceSubstitutionModel
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toString
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report
Description copied from interface:Report
print human readable report (e.g., on parameters and associated model)
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