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java.lang.Objectpal.misc.PalObjectListener.EventGenerator
pal.substmodel.YangCodonModel.SimplePositiveSelection
public static class YangCodonModel.SimplePositiveSelection
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.
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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YangCodonModel.SimplePositiveSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double startingFreeOmega)
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YangCodonModel.SimplePositiveSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double startingFreeOmega,
double p0,
double p1)
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YangCodonModel.SimplePositiveSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double startingFreeOmega,
double p0,
double p1,
double p2)
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protected |
YangCodonModel.SimplePositiveSelection(YangCodonModel.SimplePositiveSelection toCopy)
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Method Summary | |
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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 |
getDefaultValue(int n)
get default value of parameter |
double[] |
getEquilibriumFrequencies()
Should return a double[] array of the related equilibrium frequencies. |
double |
getLowerLimit(int n)
get lower parameter limit |
int |
getNumberOfTransitionCategories()
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int |
getNumParameters()
Five parameters, three proportions, kappa, omega. |
OrthogonalHints |
getOrthogonalHints()
May return null |
double |
getParameter(int n)
get model parameter |
double[] |
getTransitionCategoryProbabilities()
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double |
getTransitionCategoryProbability(int category)
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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 limit |
void |
report(java.io.PrintWriter pw)
print human readable report (e.g., on parameters and associated model) |
void |
setParameter(double param,
int n)
set model parameter |
void |
setParameterSE(double paramSE,
int n)
set standard errors for model parameter |
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) |
java.lang.String |
toString()
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Methods inherited from class pal.misc.PalObjectListener.EventGenerator |
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addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener |
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.substmodel.SubstitutionModel |
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addPalObjectListener, removePalObjectListener |
Constructor Detail |
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protected YangCodonModel.SimplePositiveSelection(YangCodonModel.SimplePositiveSelection toCopy)
public YangCodonModel.SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega)
public YangCodonModel.SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1)
public YangCodonModel.SimplePositiveSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double startingFreeOmega, double p0, double p1, double p2)
Method Detail |
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public java.lang.Object clone()
clone
in interface SubstitutionModel
clone
in class java.lang.Object
public SubstitutionModel getCopy()
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[][][] tableStore)
SubstitutionModel
getTransitionProbabilities
in interface SubstitutionModel
public void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
getTransitionProbabilities
in interface SubstitutionModel
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
getTransitionProbabilitiesTranspose
in interface SubstitutionModel
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
getTransitionProbabilitiesTranspose
in interface SubstitutionModel
public final void setTransitionCategoryProbabilities(double p0, double p1, double p2)
p0
- p1
- p2
- public int getNumParameters()
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
public OrthogonalHints getOrthogonalHints()
SubstitutionModel
getOrthogonalHints
in interface SubstitutionModel
public java.lang.String toString()
toString
in class java.lang.Object
public void report(java.io.PrintWriter pw)
Report
report
in interface Report
pw
- output stream
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