public class VariableIndependentSingleSplitDistribution extends java.lang.Object implements SingleSplitDistribution
Title: VariableIndependentSingleSplitDistribution
Description: Allows for a split in substitution model parameters where the class distribution before the split maybe different after the split (and the probabilities of being in a before class and an after class are independent)
Constructor and Description |
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VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories) |
VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories,
double[] initialParameters) |
Modifier and Type | Method and Description |
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void |
getDefaultValues(double[] store,
int startIndex)
get default value parameter values
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double[] |
getDistribution() |
double[][] |
getDistributionInfo()
Obtain the distribution information stored in the following format: [beforeclass][afterclass]
For example, the probability of evolving in class 0 before the split, and class 1 after the split - [0][1]
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double |
getLowerLimit(int n)
get lower parameter limit
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int |
getNumberOfBaseTransitionCategories() |
int |
getNumberOfParameters()
get number of parameters
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void |
getParameters(double[] store,
int startIndex)
get model parameter
|
double |
getUpperLimit(int n)
get upper parameter limit
|
void |
setParameters(double[] store,
int startIndex)
set model parameter
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java.lang.String |
toString() |
public VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories)
public VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories, double[] initialParameters)
public double[] getDistribution()
public int getNumberOfBaseTransitionCategories()
getNumberOfBaseTransitionCategories
in interface SingleSplitDistribution
public double[][] getDistributionInfo()
SingleSplitDistribution
getDistributionInfo
in interface SingleSplitDistribution
public int getNumberOfParameters()
NeoParameterized
getNumberOfParameters
in interface NeoParameterized
public void setParameters(double[] store, int startIndex)
NeoParameterized
setParameters
in interface NeoParameterized
store
- the array holding the parametersstartIndex
- the index into the array that the related parameters start atpublic void getParameters(double[] store, int startIndex)
NeoParameterized
getParameters
in interface NeoParameterized
startIndex
- the index into the array that the related parameters start atpublic double getLowerLimit(int n)
NeoParameterized
getLowerLimit
in interface NeoParameterized
n
- parameter numberpublic double getUpperLimit(int n)
NeoParameterized
getUpperLimit
in interface NeoParameterized
n
- parameter numberpublic void getDefaultValues(double[] store, int startIndex)
NeoParameterized
getDefaultValues
in interface NeoParameterized
public java.lang.String toString()
toString
in class java.lang.Object