org.biojava.bio.dp
Interface EmissionState

All Known Implementing Classes:
SimpleEmissionState

public interface EmissionState
extends State, Trainable

A state in a markov process that has an emission spectrum.

These states have an associated Distribution. Within an HMM, these are the states that actualy make your observed sequence. They also must supply training behaviour to set the emission spectrum up.

Author:
Matthew Pocock

Method Summary
 int[] getAdvance()
          Determine the number of symbols this state advances along one or more symbol lists.
 Distribution getDistribution()
          Get the Distribution associated with this state.
 void setDistribution(Distribution dis)
          Set the Distribution associated with this state.
 
Methods inherited from interface org.biojava.bio.dp.Trainable
registerWithTrainer
 
Methods inherited from interface org.biojava.bio.symbol.AtomicSymbol
getMatches
 
Methods inherited from interface org.biojava.bio.symbol.Symbol
getName, getToken
 
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
 

Method Detail

getAdvance

public int[] getAdvance()
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.


getDistribution

public Distribution getDistribution()
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.

Returns:
the current Distribution object used by this state

setDistribution

public void setDistribution(Distribution dis)
                     throws java.lang.UnsupportedOperationException
Set the Distribution associated with this state.
Parameters:
dis - the new Distribution to use