org.biojava.bio.dp
Class SimpleEmissionState

java.lang.Object
  |
  +--org.biojava.bio.dp.SimpleEmissionState
Direct Known Subclasses:
MagicalState

public class SimpleEmissionState
extends java.lang.Object
implements EmissionState, java.io.Serializable

See Also:
Serialized Form

Constructor Summary
SimpleEmissionState(java.lang.String name, Annotation ann, int[] advance, Distribution dis)
           
 
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)
           
 void setAnnotation(Annotation ann)
           
 void setDistribution(Distribution dis)
          Set the Distribution associated with this state.
 void setName(java.lang.String name)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SimpleEmissionState

public SimpleEmissionState(java.lang.String name,
                           Annotation ann,
                           int[] advance,
                           Distribution dis)
Method Detail

getAnnotation

public final Annotation getAnnotation()
Description copied from interface: Annotatable
Should return the associated annotation object.
Tags copied from interface: Annotatable
Returns:
an Annotation object, never null

setAnnotation

public final void setAnnotation(Annotation ann)

getDistribution

public final Distribution getDistribution()
Description copied from interface: EmissionState
Get the Distribution associated with this state.

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.

Specified by:
getDistribution in interface EmissionState
Tags copied from interface: EmissionState
Returns:
the current Distribution object used by this state

setDistribution

public final void setDistribution(Distribution dis)
Description copied from interface: EmissionState
Set the Distribution associated with this state.
Specified by:
setDistribution in interface EmissionState
Tags copied from interface: EmissionState
Parameters:
dis - the new Distribution to use

getAdvance

public int[] getAdvance()
Description copied from interface: EmissionState
Determine the number of symbols this state advances along one or more symbol lists. In the simple case, this method should almost always return {1} if it is a true `emmision' state, or {0} if it is a dot state which only emits a gap character. For pairwise HMMs, it will normally return {1, 1} for match state, and {0, 1} or {1, 0} for a gap state. Under some circumstances it may be valid to return values other than 1 or 0, but you should consider the consequences for HMM architecture very carefully.

Note that the int array returned by this method should never be modified.

Specified by:
getAdvance in interface EmissionState

setAdvance

public void setAdvance(int[] advance)

getToken

public char getToken()
Description copied from interface: Symbol
The token for the symbol.
Tags copied from interface: Symbol
Returns:
the token

getName

public final java.lang.String getName()
Description copied from interface: Symbol
The long name for the symbol.
Tags copied from interface: Symbol
Returns:
the long name

setName

public final void setName(java.lang.String name)

getMatches

public Alphabet getMatches()
Description copied from interface: AtomicSymbol
Return an alphabet containing only this symbol.
Tags copied from interface: Symbol
Returns:
the Alphabet of symbols matched by this symbol

registerWithTrainer

public void registerWithTrainer(ModelTrainer trainer)
Description copied from interface: Trainable
Perform any registration that is necisary with mt.

This may include registering handelers for transition or emission counts, or registering other Trainable objects with the ModelTrainer.

Tags copied from interface: Trainable
Parameters:
mt - the ModelTrainer that encapsulates the training environment
Returns:
a StateTrainer