org.biojava.bio.program.hmmer

Class ProfileEmissionState

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dp.SimpleEmissionState

org.biojava.bio.program.hmmer.ProfileEmissionState

All Implemented Interfaces:

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

public class ProfileEmissionState
extends SimpleEmissionState

A state in a HMMer model.

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

Constructor Summary

Constructors

Constructor and Description
ProfileEmissionState(String str, Annotation ann, int[] adv, Distribution dis)

Method Summary

Modifier and Type	Method and Description
protected static double	log2(double x)
double	logProb(Symbol sym)

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

Constructor Detail

ProfileEmissionState

public ProfileEmissionState(String str,
                            Annotation ann,
                            int[] adv,
                            Distribution dis)

Method Detail

logProb

public double logProb(Symbol sym)
               throws IllegalSymbolException

Throws:

IllegalSymbolException

log2

protected static double log2(double x)