pal.substmodel
Class ConstantIndependentSingleSplitDistribution

java.lang.Object
  pal.substmodel.ConstantIndependentSingleSplitDistribution

All Implemented Interfaces:

NeoParameterized, SingleSplitDistribution

public class ConstantIndependentSingleSplitDistribution
extends java.lang.Object
implements SingleSplitDistribution

Title: ConstantIndependentSingleSplitDistribution

Description: Allows for a split in substitution model parameters where the class distribution before the split is the same as after the split (and the probabilities of being in a before class and an after class are independent)

Author:

Matthew Goode

Constructor Summary

ConstantIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories)

ConstantIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories, double[] initialParameters)

Method Summary

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

ConstantIndependentSingleSplitDistribution

public ConstantIndependentSingleSplitDistribution(int numberOfBaseTransitionCategories)

ConstantIndependentSingleSplitDistribution

public ConstantIndependentSingleSplitDistribution(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