org.biojava.bio.dist

Class OrderNDistributionFactory

java.lang.Object

org.biojava.bio.dist.OrderNDistributionFactory

All Implemented Interfaces:

DistributionFactory

public class OrderNDistributionFactory
extends Object
implements DistributionFactory

Default factory for Order-N distributions.

Since:

1.1

Author:

Thomas Down, Mark Schreiber

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.dist.DistributionFactory

DistributionFactory.DefaultDistributionFactory

Field Summary

Fields

Modifier and Type	Field and Description
static DistributionFactory	DEFAULT Factory which used DistributionFactory.DEFAULT to create conditioned distributions.

Constructor Summary

Constructors

Constructor and Description
OrderNDistributionFactory(DistributionFactory df) Construct a new OrderNDistributionFactory with a specified factory for conditioned distributions.

Method Summary

Modifier and Type	Method and Description
Distribution	createDistribution(Alphabet alpha) Creates an OrderNDistribution of the appropriate type.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT

public static final DistributionFactory DEFAULT

Factory which used DistributionFactory.DEFAULT to create conditioned distributions.

Constructor Detail

OrderNDistributionFactory

public OrderNDistributionFactory(DistributionFactory df)

Construct a new OrderNDistributionFactory with a specified factory for conditioned distributions.

Parameters:

df - The DistributionFactory used for construction new conditioned distributions.

Method Detail

createDistribution

public Distribution createDistribution(Alphabet alpha)
                                throws IllegalAlphabetException

Creates an OrderNDistribution of the appropriate type.

Specified by:

createDistribution in interface DistributionFactory

Parameters:

alpha - the Alphabet should be in a form that clearly indicates the conditioning and the conditioned alphabet unless it is very obvious. For example (DNA x DNA) is obvious, ((DNA x DNA x DNA) x DNA) indicates that (DNA x DNA x DNA) is the conditioning Alphabet and DNA is the conditioned Alphabet. (DNA x DNA x DNA x DNA) doesn't but for compatibility with biojava 1.2 this is allowed in the constructor. As from biojava 1.2.3 or greater this will be internally converted to ((DNA x DNA x DNA) x DNA) which was the convention implied by biojava 1.2 Calls to the returned Distributions getAlphabet() method will return the converted Alphabet.

Returns:

An OrderNDistribution

Throws:

IllegalAlphabetException - if a Distribution cannot be made with that Alphabet.