Package org.biojava.bio.dist

Interface OrderNDistribution

All Superinterfaces:

Changeable, Distribution

All Known Implementing Classes:

AbstractOrderNDistribution

public interface OrderNDistribution
extends Distribution

Provides an N'th order distribution. This is a distribution over one alphabet which is conditioned on having previously observed one or more other symbols (potentially from different alphabets).

Order-N distributions are always over a CrossProductAlphabet.

Note: Unlike normal distributions, the total weights for all symbols in the overall alphabet do not sum to 1.0. Instead, the weights of each sub-distribution should sum to 1.0.

This would typically be used in conjunction with an OrderNSymbolList.

Since:

1.0

Author:

Thomas Down, Samiul Hasan, Matthew Pocock

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.dist.Distribution

Distribution.NullModelForwarder

Field Summary

Fields inherited from interface org.biojava.bio.dist.Distribution

NULL_MODEL, WEIGHTS

Method Summary

Modifier and Type	Method	Description
Collection	conditionedDistributions()	Get the conditioned distributions.
Alphabet	getConditionedAlphabet()	Get the conditioned alphabet.
Alphabet	getConditioningAlphabet()	Get the conditioning alphabet of this distribution.
Distribution	getDistribution(Symbol sym)
void	setDistribution(Symbol sym, Distribution dist)	Set the distribution assocated with a symbol.

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.dist.Distribution

getAlphabet, getNullModel, getWeight, registerWithTrainer, sampleSymbol, setNullModel, setWeight

Method Detail

getConditioningAlphabet

Alphabet getConditioningAlphabet()

Get the conditioning alphabet of this distribution. If the `overall' alphabet is a cross-product of two alphabets, this will be the first of those alphabets. If it is a cross-product of more than two alphabets, the conditioning alphabet is the cross-product of all but the last alphabet.

Returns:

the conditioning Alphabet

getConditionedAlphabet

Alphabet getConditionedAlphabet()

Get the conditioned alphabet. This is the last alphabet in the distribution's overall cross-product. It will be the alphabet of all the sub-distributions contained within this OrderNDistribution.

Returns:

the conditioned Alphabet

conditionedDistributions

Collection conditionedDistributions()

Get the conditioned distributions.

Returns:

the conditioned distributions

setDistribution

void setDistribution(Symbol sym,
                     Distribution dist)
              throws IllegalSymbolException,
                     IllegalAlphabetException

Set the distribution assocated with a symbol.

Parameters:

sym - the symbol in the conditioning Alphabet

dist - a distribution over the conditioned Alphabet

Throws:

IllegalSymbolException - if sym is not in the conditioning Alphabet

IllegalAlphabetException - if dist is not over the conditioned Alphabet

getDistribution

Distribution getDistribution(Symbol sym)
                      throws IllegalSymbolException

Throws:

IllegalSymbolException