org.biojava.bio.program.hmmer
Class ProfileEmissionState

java.lang.Object
  extended byorg.biojava.utils.AbstractChangeable
      extended byorg.biojava.bio.dp.SimpleEmissionState
          extended byorg.biojava.bio.program.hmmer.ProfileEmissionState
All Implemented Interfaces:
Annotatable, AtomicSymbol, BasisSymbol, Changeable, EmissionState, java.io.Serializable, State, Symbol, Trainable

public class ProfileEmissionState
extends SimpleEmissionState

A state in a HMMer model.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes inherited from class org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
 
Fields inherited from class org.biojava.bio.dp.SimpleEmissionState
annotationForwarder
 
Fields inherited from interface org.biojava.bio.dp.EmissionState
ADVANCE, DISTRIBUTION
 
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
 
Constructor Summary
ProfileEmissionState(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
           
 
Method Summary
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, 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(java.lang.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)