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java.lang.Objectpal.misc.PalObjectListener.EventGenerator
pal.substmodel.YangCodonModel.SimpleNeutralSelection
public static class YangCodonModel.SimpleNeutralSelection
A Substitution Model which can be used to implment the Neutral Model (with out continuous rate stuff)
Codon model of [1] which uses the weighted sum of trwo base YangCodon models where
omega=0, omega=1 repectively
[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 |
Field Summary | |
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static double |
P_DEFAULT_VALUE
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static double |
P_LOWER_LIMIT
|
static double |
P_UPPER_LIMIT
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Constructor Summary | |
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YangCodonModel.SimpleNeutralSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa)
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YangCodonModel.SimpleNeutralSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double proportionZero)
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Method Summary | |
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java.lang.Object |
clone()
|
SubstitutionModel |
getCopy()
|
DataType |
getDataType()
|
double |
getDefaultValue(int n)
get default value of parameter |
double[] |
getEquilibriumFrequencies()
Should return a double[] array of the related equilibrium frequencies. |
double[] |
getEquilibriumProbabilities()
|
double |
getLowerLimit(int n)
get lower parameter limit |
int |
getNumberOfTransitionCategories()
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int |
getNumParameters()
Two parameters, kappa, p, |
OrthogonalHints |
getOrthogonalHints()
May return null |
double |
getParameter(int n)
get model parameter |
double[] |
getTransitionCategoryProbabilities()
|
double |
getTransitionCategoryProbability(int category)
|
void |
getTransitionProbabilities(double branchLength,
double[][][] tableStore)
Table is organized as [tree_group][from][to] |
void |
getTransitionProbabilities(double branchLength,
int category,
double[][] tableStore)
Table is organized as [transition_group][from][to] |
void |
getTransitionProbabilitiesTranspose(double branchLength,
double[][][] tableStore)
Table is organized as [transition_group][to][from] |
void |
getTransitionProbabilitiesTranspose(double branchLength,
int category,
double[][] tableStore)
Table is organized as [transition_group][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 |
java.lang.String |
toString()
|
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 |
Field Detail |
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public static final double P_UPPER_LIMIT
public static final double P_LOWER_LIMIT
public static final double P_DEFAULT_VALUE
Constructor Detail |
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public YangCodonModel.SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa)
public YangCodonModel.SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double proportionZero)
Method Detail |
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public java.lang.Object clone()
clone
in interface SubstitutionModel
clone
in class java.lang.Object
public double[] getEquilibriumFrequencies()
SubstitutionModel
getEquilibriumFrequencies
in interface SubstitutionModel
public SubstitutionModel getCopy()
public double[] getEquilibriumProbabilities()
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 void getTransitionProbabilities(double branchLength, double[][][] tableStore)
getTransitionProbabilities
in interface SubstitutionModel
public void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
SubstitutionModel
getTransitionProbabilities
in interface SubstitutionModel
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
SubstitutionModel
getTransitionProbabilitiesTranspose
in interface SubstitutionModel
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
SubstitutionModel
getTransitionProbabilitiesTranspose
in interface SubstitutionModel
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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