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

Nested Classes

Modifier and Type	Interface and Description
static class	DistributionFactory.DefaultDistributionFactory The default DistributionFactory implementation.

Field Summary

Fields

Modifier and Type	Field and Description
static DistributionFactory	DEFAULT The default DistributionFactory object.

Method Summary

Methods

Modifier and Type	Method and Description
Distribution	createDistribution(Alphabet alpha) Generate a new Distribution as requested.

Field Detail

DEFAULT

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

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