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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.dp.SimpleEmissionState
org.biojava.bio.program.hmmer.ProfileEmissionState
A state in a HMMer model.
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)
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Method Summary | |
protected static double |
log2(double x)
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double |
logProb(Symbol sym)
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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 |
public ProfileEmissionState(java.lang.String str, Annotation ann, int[] adv, Distribution dis)
Method Detail |
public double logProb(Symbol sym) throws IllegalSymbolException
IllegalSymbolException
protected static double log2(double x)
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