org.biojava.bio.dp
Interface EmissionState

All Superinterfaces:
Annotatable, AtomicSymbol, BasisSymbol, Changeable, State, Symbol, Trainable
All Known Implementing Classes:
MagicalState, ProfileEmissionState, SimpleEmissionState

public interface EmissionState
extends State, Trainable, Changeable

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

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
 
Field Summary
static ChangeType ADVANCE
           This signals that the advance array has been altered.
static ChangeType DISTRIBUTION
           This signals that the distribution associate with an EmissionState has been altered.
 
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
 
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 setAdvance(int[] advance)
          Set the advance array.
 void setDistribution(Distribution dis)
          Set the Distribution associated with this state.
 
Methods inherited from interface org.biojava.bio.symbol.BasisSymbol
getSymbols
 
Methods inherited from interface org.biojava.bio.symbol.Symbol
getMatches, getName
 
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
 
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
 
Methods inherited from interface org.biojava.bio.dp.Trainable
registerWithTrainer
 

Field Detail

DISTRIBUTION

static final ChangeType DISTRIBUTION

This signals that the distribution associate with an EmissionState has been altered.

If the distribution has changed its weights, then the event'e getChainedEvent method will return the event fired by the distribution. If one distribution has been replaced by another, then the new and old Distributions will be in current and previous, respectively.


ADVANCE

static final ChangeType ADVANCE

This signals that the advance array has been altered.

current and previous should hold the current and previous advances, respectively.

Method Detail

getAdvance

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, and contact the authors.

For developers:
you may wish to return a copy of some underlying array from this method as code outside could modify the array you give

setAdvance

void setAdvance(int[] advance)
                throws ChangeVetoException
Set the advance array.

Parameters:
advance - an array of ints, specifying how many symbols are consumed from each sequence
Throws:
ChangeVetoException - if the implementation doesn't support setting advance, or if the change is vetoed

getDistribution

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

void setDistribution(Distribution dis)
                     throws ChangeVetoException
Set the Distribution associated with this state.

Parameters:
dis - the new Distribution to use
Throws:
ChangeVetoException - if the implementation doesn't support setting the distribution, or if the change is vetoed