java.io.Serializable
, Parameterized
, Report
, SubstitutionModel
public static class YangCodonModel.SimpleNeutralSelection extends PalObjectListener.EventGenerator implements SubstitutionModel
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
SubstitutionModel.Utils
Modifier and Type | Field | Description |
---|---|---|
static double |
P_DEFAULT_VALUE |
|
static double |
P_LOWER_LIMIT |
|
static double |
P_UPPER_LIMIT |
Constructor | Description |
---|---|
SimpleNeutralSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa) |
|
SimpleNeutralSelection(CodonTable translator,
double[] codonProbabilities,
double startingKappa,
double proportionZero) |
Modifier and Type | Method | Description |
---|---|---|
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() |
|
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() |
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
addPalObjectListener, fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent, removePalObjectListener
addPalObjectListener, removePalObjectListener
public static final double P_UPPER_LIMIT
public static final double P_LOWER_LIMIT
public static final double P_DEFAULT_VALUE
public SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa)
public SimpleNeutralSelection(CodonTable translator, double[] codonProbabilities, double startingKappa, double proportionZero)
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 numberpublic 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 numberpublic double getUpperLimit(int n)
Parameterized
getUpperLimit
in interface Parameterized
n
- parameter numberpublic double getDefaultValue(int n)
Parameterized
getDefaultValue
in interface Parameterized
n
- parameter numberpublic OrthogonalHints getOrthogonalHints()
SubstitutionModel
getOrthogonalHints
in interface SubstitutionModel
public java.lang.String toString()
toString
in class java.lang.Object