org.biojava.bio.dist
Class OrderNDistributionFactory

java.lang.Object
  extended by 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
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.