VariableIndependentSingleSplitDistribution

java.lang.Object
- pal.substmodel.VariableIndependentSingleSplitDistribution

All Implemented Interfaces:

NeoParameterized, SingleSplitDistribution
```
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)

Author:

Matthew Goode

Constructor Summary

Constructors
Constructor	Description
`VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories)`
`VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories, double[] initialParameters)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`getDefaultValues(double[] store, int startIndex)`	get default value parameter values
`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]
`double`	`getLowerLimit(int n)`	get lower parameter limit
`int`	`getNumberOfBaseTransitionCategories()`
`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()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - VariableIndependentSingleSplitDistribution
```
public VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories)
```
  - VariableIndependentSingleSplitDistribution
```
public VariableIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories,
                                                  double[] initialParameters)
```
- Method Detail
  - getDistribution
```
public double[] getDistribution()
```
  - getNumberOfBaseTransitionCategories
```
public int getNumberOfBaseTransitionCategories()
```
    Specified by:
    
    getNumberOfBaseTransitionCategories in interface SingleSplitDistribution
  - 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 interface SingleSplitDistribution
    
    Returns:
    
    an appropriate matrix representing the probability of evolving in the different combinations of before and after classes
  - getNumberOfParameters
```
public int getNumberOfParameters()
```
    Description copied from interface: NeoParameterized
    
    get number of parameters
    
    Specified by:
    
    getNumberOfParameters in interface NeoParameterized
    
    Returns:
    
    number of parameters
  - setParameters
```
public void setParameters(double[] store,
                          int startIndex)
```
    Description copied from interface: NeoParameterized
    
    set model parameter
    
    Specified by:
    
    setParameters in interface NeoParameterized
    
    Parameters:
    
    store - the array holding the parameters
    
    startIndex - the index into the array that the related parameters start at
  - getParameters
```
public void getParameters(double[] store,
                          int startIndex)
```
    Description copied from interface: NeoParameterized
    
    get model parameter
    
    Specified by:
    
    getParameters in interface NeoParameterized
    
    startIndex - the index into the array that the related parameters start at
  - getLowerLimit
```
public double getLowerLimit(int n)
```
    Description copied from interface: NeoParameterized
    
    get lower parameter limit
    
    Specified by:
    
    getLowerLimit in interface NeoParameterized
    
    Parameters:
    
    n - parameter number
    
    Returns:
    
    lower bound
  - getUpperLimit
```
public double getUpperLimit(int n)
```
    Description copied from interface: NeoParameterized
    
    get upper parameter limit
    
    Specified by:
    
    getUpperLimit in interface NeoParameterized
    
    Parameters:
    
    n - parameter number
    
    Returns:
    
    upper bound
  - getDefaultValues
```
public void getDefaultValues(double[] store,
                             int startIndex)
```
    Description copied from interface: NeoParameterized
    
    get default value parameter values
    
    Specified by:
    
    getDefaultValues in interface NeoParameterized
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object

Class VariableIndependentSingleSplitDistribution

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

VariableIndependentSingleSplitDistribution

VariableIndependentSingleSplitDistribution

Method Detail

getDistribution

getNumberOfBaseTransitionCategories

getDistributionInfo

getNumberOfParameters

setParameters

getParameters

getLowerLimit

getUpperLimit

getDefaultValues

toString