org.biojava.bio.dp

Class MagicalState

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dp.SimpleEmissionState

org.biojava.bio.dp.MagicalState

All Implemented Interfaces:

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

public final class MagicalState
extends SimpleEmissionState

Start/end state for HMMs.

All MagicalState objects emit over MAGICAL_ALPHABET, which only contains MAGICAL_STATE.

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

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

Annotatable.AnnotationForwarder

Field Summary

Fields inherited from class org.biojava.bio.dp.SimpleEmissionState

annotationForwarder, distForwarder

Fields inherited from interface org.biojava.bio.dp.EmissionState

ADVANCE, DISTRIBUTION

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Method Summary

Modifier and Type	Method and Description
static MagicalState	getMagicalState(Alphabet alphabet, int heads)

Methods inherited from class org.biojava.bio.dp.SimpleEmissionState

getAdvance, getAnnotation, getBases, getChangeSupport, getDistribution, getMatches, getName, getSymbols, getToken, registerWithTrainer, setAdvance, setAnnotation, setDistribution, setName

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Method Detail

getMagicalState

public static MagicalState getMagicalState(Alphabet alphabet,
                                           int heads)