pal.misc

Class ParameterizedDoubleBundle

java.lang.Object

pal.misc.ParameterizedDoubleBundle

All Implemented Interfaces:

NeoParameterized

public class ParameterizedDoubleBundle
extends java.lang.Object
implements NeoParameterized

Title: ParameterizedDoubleBundle

Description: A parameterized double bundle is simple a parameterized collection of mutable double objects. The idea is, all the changable attributes of the phylogenetic entities that are being accessed (eg the branch lengths of a tree, and the parameters of a model) can be grouped together externally (the point of this approach will become more apparent over time as PAL evolves)

Version:

1.0

Author:

Matthew Goode

Constructor Summary

Constructors

Constructor and Description
ParameterizedDoubleBundle(MutableDouble[] parameters)

Method Summary

Methods

Modifier and Type	Method and Description
void	getDefaultValues(double[] store, int startIndex) get default value parameter values
double	getLowerLimit(int n) get lower parameter limit
int	getNumberOfParameters() get number of parameters
void	getParameters(double[] parameterStore, int startIndex) get model parameter
double	getUpperLimit(int n) get upper parameter limit
void	setParameters(double[] parameters, 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

ParameterizedDoubleBundle

public ParameterizedDoubleBundle(MutableDouble[] parameters)

Method Detail

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[] parameters,
                 int startIndex)

Description copied from interface: NeoParameterized

set model parameter

Specified by:

setParameters in interface NeoParameterized

Parameters:

parameters - the array holding the parameters

startIndex - the index into the array that the related parameters start at

getParameters

public void getParameters(double[] parameterStore,
                 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