org.biojava.bio.dp

Class SimpleEmissionState

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.dp.SimpleEmissionState

All Implemented Interfaces:

Serializable, Annotatable, EmissionState, State, Trainable, AtomicSymbol, BasisSymbol, Symbol, Changeable

Direct Known Subclasses:

MagicalState, ProfileEmissionState

public class SimpleEmissionState
extends AbstractChangeable
implements EmissionState, Serializable

Author:

Matthew Pocock, Thomas Down, Mark Schreiber

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
protected ChangeForwarder	annotationForwarder
protected ChangeForwarder	distForwarder

Fields inherited from interface org.biojava.bio.dp.EmissionState

ADVANCE, DISTRIBUTION

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Constructor and Description
SimpleEmissionState(String name, Annotation ann, int[] advance, Distribution dis)

Method Summary

Modifier and Type	Method and Description
int[]	getAdvance() Determine the number of symbols this state advances along one or more symbol lists.
Annotation	getAnnotation() Should return the associated annotation object.
Set	getBases()
protected ChangeSupport	getChangeSupport(ChangeType ct) Called to retrieve the ChangeSupport for this object.
Distribution	getDistribution() Get the Distribution associated with this state.
Alphabet	getMatches() The alphabet containing the symbols matched by this ambiguity symbol.
String	getName() The long name for the symbol.
List	getSymbols() The list of symbols that this symbol is composed from.
char	getToken()
void	registerWithTrainer(ModelTrainer trainer) Perform any registration that is necessary with mt.
void	setAdvance(int[] advance) Set the advance array.
void	setAnnotation(Annotation ann)
void	setDistribution(Distribution dis) Set the Distribution associated with this state.
void	setName(String name)

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, 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

Field Detail

annotationForwarder

protected transient ChangeForwarder annotationForwarder

distForwarder

protected transient ChangeForwarder distForwarder

Constructor Detail

SimpleEmissionState

public SimpleEmissionState(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.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation object, never null

setAnnotation

public final void setAnnotation(Annotation ann)
                         throws ChangeVetoException

Throws:

ChangeVetoException

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

Returns:

the current Distribution object used by this state

setDistribution

public final void setDistribution(Distribution dis)
                           throws ChangeVetoException

Description copied from interface: EmissionState

Set the Distribution associated with this state.

Specified by:

setDistribution in interface EmissionState

Parameters:

dis - the new Distribution to use

Throws:

ChangeVetoException - if the implementation doesn't support setting the distribution, or if the change is vetoed

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, and contact the authors. Developers may wish to return a copy of some underlying array from this method as code outside could modify the array you give

Specified by:

getAdvance in interface EmissionState

setAdvance

public void setAdvance(int[] advance)
                throws ChangeVetoException

Description copied from interface: EmissionState

Set the advance array.

Specified by:

setAdvance in interface EmissionState

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

getToken

public char getToken()

getName

public final String getName()

Description copied from interface: Symbol

The long name for the symbol.

Specified by:

getName in interface Symbol

Returns:

the long name

setName

public final void setName(String name)

getMatches

public Alphabet getMatches()

Description copied from interface: Symbol

The alphabet containing the symbols matched by this ambiguity symbol.

This alphabet contains all of, and only, the symbols matched by this symbol. For example, the symbol representing the DNA ambiguity code for W would contain the symbol for A and T from the DNA alphabet.

Specified by:

getMatches in interface Symbol

Returns:

the Alphabet of symbols matched by this symbol

getBases

public Set getBases()

getSymbols

public List getSymbols()

Description copied from interface: BasisSymbol

The list of symbols that this symbol is composed from.

In the usual case, this list will contain just this single symbol. In the case where a symbol represents an ordered combination of other symbols, the list will contain each of these BasisSymbols.

Specified by:

getSymbols in interface BasisSymbol

Returns:

the List of Symbols that this Symbol is built from

registerWithTrainer

public void registerWithTrainer(ModelTrainer trainer)

Description copied from interface: Trainable

Perform any registration that is necessary with mt.

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

Specified by:

registerWithTrainer in interface Trainable

Parameters:

trainer - the ModelTrainer that encapsulates the training environment

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable