Package 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

  • Field Details

    • DEFAULT

      public static final DistributionFactory DEFAULT
      Factory which used DistributionFactory.DEFAULT to create conditioned distributions.

  • Constructor Details

    • 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 Details

    • 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.