public interface SubstitutionModel extends Parameterized, Report, java.io.Serializable
Modifier and Type | Interface and Description |
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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 and Description |
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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()