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 Description

ParameterizedDoubleBundle(MutableDouble[] parameters)

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`	`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

Class ParameterizedDoubleBundle

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ParameterizedDoubleBundle

Method Detail

getNumberOfParameters

setParameters

getParameters

getLowerLimit

getUpperLimit

getDefaultValues

toString