Package pal.substmodel
Class SaturatedSingleSplitDistribution
java.lang.Object
pal.substmodel.SaturatedSingleSplitDistribution
- All Implemented Interfaces:
NeoParameterized
,SingleSplitDistribution
Title: SaturatedSingleSplitDistribution
Description: A model
Copyright: Copyright (c) 2003
Company:
- Version:
- 1.0
- Author:
- not attributable
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Constructor Summary
ConstructorsConstructorDescriptionSaturatedSingleSplitDistribution
(int numberOfBaseTransitionCategories) SaturatedSingleSplitDistribution
(int numberOfBaseTransitionCategories, double[] initialParameters) -
Method Summary
Modifier and TypeMethodDescriptionvoid
getDefaultValues
(double[] store, int startIndex) get default value parameter valuesdouble[]
double[][]
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 limitint
int
get number of parametersvoid
getParameters
(double[] store, int startIndex) get model parameterdouble
getUpperLimit
(int n) get upper parameter limitvoid
setParameters
(double[] store, int startIndex) set model parametertoString()
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Constructor Details
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SaturatedSingleSplitDistribution
public SaturatedSingleSplitDistribution(int numberOfBaseTransitionCategories) -
SaturatedSingleSplitDistribution
public SaturatedSingleSplitDistribution(int numberOfBaseTransitionCategories, double[] initialParameters)
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Method Details
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getDistribution
public double[] getDistribution() -
getNumberOfBaseTransitionCategories
public int getNumberOfBaseTransitionCategories()- Specified by:
getNumberOfBaseTransitionCategories
in interfaceSingleSplitDistribution
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getDistributionInfo
public double[][] getDistributionInfo()Description copied from interface:SingleSplitDistribution
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]- Specified by:
getDistributionInfo
in interfaceSingleSplitDistribution
- Returns:
- an appropriate matrix representing the probability of evolving in the different combinations of before and after classes
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getNumberOfParameters
public int getNumberOfParameters()Description copied from interface:NeoParameterized
get number of parameters- Specified by:
getNumberOfParameters
in interfaceNeoParameterized
- Returns:
- number of parameters
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setParameters
public void setParameters(double[] store, int startIndex) Description copied from interface:NeoParameterized
set model parameter- Specified by:
setParameters
in interfaceNeoParameterized
- Parameters:
store
- the array holding the parametersstartIndex
- the index into the array that the related parameters start at
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getParameters
public void getParameters(double[] store, int startIndex) Description copied from interface:NeoParameterized
get model parameter- Specified by:
getParameters
in interfaceNeoParameterized
- Parameters:
startIndex
- the index into the array that the related parameters start at
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getLowerLimit
public double getLowerLimit(int n) Description copied from interface:NeoParameterized
get lower parameter limit- Specified by:
getLowerLimit
in interfaceNeoParameterized
- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
public double getUpperLimit(int n) Description copied from interface:NeoParameterized
get upper parameter limit- Specified by:
getUpperLimit
in interfaceNeoParameterized
- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValues
public void getDefaultValues(double[] store, int startIndex) Description copied from interface:NeoParameterized
get default value parameter values- Specified by:
getDefaultValues
in interfaceNeoParameterized
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toString
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