org.biojava.bio.program.hmmer.ProfileEmissionState

All Implemented Interfaces:: Serializable, Annotatable, EmissionState, State, Trainable, AtomicSymbol, BasisSymbol, Symbol, Changeable

A state in a HMMer model.

See Also:

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.Annotatable
ANNOTATION

Fields inherited from interface org.biojava.bio.dp.EmissionState
ADVANCE, DISTRIBUTION
Constructor Summary

Constructors

Constructor

Description

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

Modifier and Type

Method

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 Details
- ProfileEmissionState
  
  public ProfileEmissionState(String str, Annotation ann, int[] adv, Distribution dis)
Method Details
- logProb
  
  public double logProb(Symbol sym) throws IllegalSymbolException
  
  Throws:
  
  IllegalSymbolException
- log2
  
  protected static double log2(double x)

Class ProfileEmissionState

Nested Class Summary