org.biojava.bio.dist
Class OrderNDistributionFactory

java.lang.Object
  |
  +--org.biojava.bio.dist.OrderNDistributionFactory

All Implemented Interfaces:

DistributionFactory

public class OrderNDistributionFactory

extends java.lang.Object

implements DistributionFactory

Default factory for Order-N distributions.

Author:

Thomas Down, Mark Schreiber

Nested Class Summary

Nested classes inherited from class org.biojava.bio.dist.DistributionFactory

DistributionFactory.DefaultDistributionFactory

Field Summary

static DistributionFactory

DEFAULT Factory which used DistributionFactory.DEFAULT to create conditioned distributions.

Constructor Summary

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

Method Summary

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.