org.biojava.bio.dist
Interface DistributionFactory

All Known Implementing Classes:

DistributionFactory.DefaultDistributionFactory, OrderNDistributionFactory

public interface DistributionFactory

A thing that can make Distributions.

This decouples programs from needing to know what implementation of Distribution to instantiate for a given alphabet. It also lets you parameterise model creation for things like profile HMMs.

Since:

1.0

Author:

Matthew Pocock

Nested Class Summary

static class

DistributionFactory.DefaultDistributionFactory The default DistributionFactory implementation.

Field Summary

static DistributionFactory

DEFAULT The default DistributionFactory object.

Method Summary

Distribution

createDistribution(Alphabet alpha) Generate a new Distribution as requested.

Field Detail

DEFAULT

public static final DistributionFactory DEFAULT

The default DistributionFactory object.

You may wish to alias this within your scripts with something like: DistributionFactory dFact = DistributionFactory.DEFAULT; dFact.createDistribution(...);

Method Detail

createDistribution

public Distribution createDistribution(Alphabet alpha)
                                throws IllegalAlphabetException

Generate a new Distribution as requested.

Parameters:

alpha - the emission alphabet for the state

Returns:

a new Distribution instance

Throws:

IllegalAlphabetException - if the factory is unable to generate a distribution for the required alphabet