Class OrderNDistributionFactory

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