org.biojava.bio.dp

Interface EmissionState

All Superinterfaces:

Annotatable, AtomicSymbol, BasisSymbol, Changeable, State, Symbol, Trainable

All Known Implementing Classes:

MagicalState, ProfileEmissionState, SimpleEmissionState

public interface EmissionState
extends State, Trainable, Changeable

A state in a markov process that has an emission spectrum.

These states have an associated Distribution. Within an HMM, these are the states that actualy make your observed sequence. They also must supply training behaviour to set the emission spectrum up.

Author:

Matthew Pocock

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
static ChangeType	ADVANCE This signals that the advance array has been altered.
static ChangeType	DISTRIBUTION This signals that the distribution associate with an EmissionState has been altered.

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Methods

Modifier and Type	Method and Description
int[]	getAdvance() Determine the number of symbols this state advances along one or more symbol lists.
Distribution	getDistribution() Get the Distribution associated with this state.
void	setAdvance(int[] advance) Set the advance array.
void	setDistribution(Distribution dis) Set the Distribution associated with this state.

Methods inherited from interface org.biojava.bio.symbol.BasisSymbol

getSymbols

Methods inherited from interface org.biojava.bio.symbol.Symbol

getMatches, getName

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.dp.Trainable

registerWithTrainer

Field Detail

DISTRIBUTION

static final ChangeType DISTRIBUTION

This signals that the distribution associate with an EmissionState has been altered.

If the distribution has changed its weights, then the event'e getChainedEvent method will return the event fired by the distribution. If one distribution has been replaced by another, then the new and old Distributions will be in current and previous, respectively.

ADVANCE

static final ChangeType ADVANCE

This signals that the advance array has been altered.

current and previous should hold the current and previous advances, respectively.

Method Detail

getAdvance

int[] getAdvance()

Determine the number of symbols this state advances along one or more symbol lists. In the simple case, this method should almost always return {1} if it is a true `emmision' state, or {0} if it is a dot state which only emits a gap character. For pairwise HMMs, it will normally return {1, 1} for match state, and {0, 1} or {1, 0} for a gap state. Under some circumstances it may be valid to return values other than 1 or 0, but you should consider the consequences for HMM architecture very carefully, and contact the authors. Developers may wish to return a copy of some underlying array from this method as code outside could modify the array you give

setAdvance

void setAdvance(int[] advance)
                throws ChangeVetoException

Set the advance array.

Parameters:

advance - an array of ints, specifying how many symbols are consumed from each sequence

Throws:

ChangeVetoException - if the implementation doesn't support setting advance, or if the change is vetoed

getDistribution

Distribution getDistribution()

Get the Distribution associated with this state.

If the state is to be added to an HMM, then the state's emission spectrum must be compatible with the HMM - that is, their emission alphabets must match.

Returns:

the current Distribution object used by this state

setDistribution

void setDistribution(Distribution dis)
                     throws ChangeVetoException

Set the Distribution associated with this state.

Parameters:

dis - the new Distribution to use

Throws:

ChangeVetoException - if the implementation doesn't support setting the distribution, or if the change is vetoed