Parameterized
, Report
, java.io.Serializable
GeneralRateDistributionSubstitutionModel
, SingleClassSubstitutionModel
, YangCodonModel.SimpleNeutralSelection
, YangCodonModel.SimplePositiveSelection
public interface SubstitutionModel extends Parameterized, Report, java.io.Serializable
Modifier and Type | Interface | Description |
---|---|---|
static class |
SubstitutionModel.Utils |
A small Utility class for things relating to Substitution Models in general
|
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
Modifier and Type | Method | Description |
---|---|---|
void |
addPalObjectListener(PalObjectListener l) |
|
java.lang.Object |
clone() |
|
DataType |
getDataType() |
|
double[] |
getEquilibriumFrequencies() |
Should return a double[] array of the related equilibrium frequencies.
|
int |
getNumberOfTransitionCategories() |
|
OrthogonalHints |
getOrthogonalHints() |
May return null
|
double[] |
getTransitionCategoryProbabilities() |
|
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 [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]
|
void |
removePalObjectListener(PalObjectListener l) |
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
DataType getDataType()
int getNumberOfTransitionCategories()
double getTransitionCategoryProbability(int category)
double[] getTransitionCategoryProbabilities()
void getTransitionProbabilities(double branchLength, double[][][] tableStore)
void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
double[] getEquilibriumFrequencies()
void addPalObjectListener(PalObjectListener l)
void removePalObjectListener(PalObjectListener l)
OrthogonalHints getOrthogonalHints()
java.lang.Object clone()