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java.lang.Objectpal.substmodel.VariableIndependentSingleSplitDistribution
public class VariableIndependentSingleSplitDistribution
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 Summary | |
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VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories)
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VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories,
double[] initialParameters)
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Method Summary | |
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void |
getDefaultValues(double[] store,
int startIndex)
get default value parameter values |
double[] |
getDistribution()
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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] |
double |
getLowerLimit(int n)
get lower parameter limit |
int |
getNumberOfBaseTransitionCategories()
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int |
getNumberOfParameters()
get number of parameters |
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 |
java.lang.String |
toString()
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories)
public VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories, double[] initialParameters)
Method Detail |
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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 number
public double getUpperLimit(int n)
NeoParameterized
getUpperLimit
in interface NeoParameterized
n
- parameter number
public void getDefaultValues(double[] store, int startIndex)
NeoParameterized
getDefaultValues
in interface NeoParameterized
public java.lang.String toString()
toString
in class java.lang.Object
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