SimpleEmissionState (BioJava-1.5-beta API)
Keywords: org.biojava.bio.dp.SimpleEmissionState class

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## 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
`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
`SimpleEmissionState(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.
`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.

  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`

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