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java.lang.Object | +--org.biojava.bio.dp.SimpleEmissionState
Constructor Summary | |
SimpleEmissionState(java.lang.String name,
Annotation ann,
int[] advance,
Distribution dis)
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Method Summary | |
int[] |
getAdvance()
Determine the number of symbols this state advances along one or more symbol lists. |
Annotation |
getAnnotation()
Should return the associated annotation object. |
Distribution |
getDistribution()
Get the Distribution associated with this state. |
Alphabet |
getMatches()
Return an alphabet containing only this symbol. |
java.lang.String |
getName()
The long name for the symbol. |
char |
getToken()
The token for the symbol. |
void |
registerWithTrainer(ModelTrainer trainer)
Perform any registration that is necisary with mt. |
void |
setAdvance(int[] advance)
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void |
setAnnotation(Annotation ann)
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void |
setDistribution(Distribution dis)
Set the Distribution associated with this state. |
void |
setName(java.lang.String name)
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Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
Constructor Detail |
public SimpleEmissionState(java.lang.String name, Annotation ann, int[] advance, Distribution dis)
Method Detail |
public final Annotation getAnnotation()
public final void setAnnotation(Annotation ann)
public final Distribution getDistribution()
If the state is to be added to an HMM, then the state's emission spectrum must be compatible with the HMM - that is, their emission alphabets must match.
public final void setDistribution(Distribution dis)
dis
- the new Distribution to usepublic int[] getAdvance()
Note that the int array returned by this method should never be modified.
public void setAdvance(int[] advance)
public char getToken()
public final java.lang.String getName()
public final void setName(java.lang.String name)
public Alphabet getMatches()
public void registerWithTrainer(ModelTrainer trainer)
This may include registering handelers for transition or emission counts, or registering other Trainable objects with the ModelTrainer.
mt
- the ModelTrainer that encapsulates the training environment
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