AbstractOrderNDistribution (BioJava-1.5-beta API)
Keywords: org.biojava.bio.dist.AbstractOrderNDistribution class

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## org.biojava.bio.dist
Class AbstractOrderNDistribution

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.dist.AbstractDistribution
              org.biojava.bio.dist.AbstractOrderNDistribution

All Implemented Interfaces:
  Serializable, Distribution, OrderNDistribution, Changeable

    public abstract class AbstractOrderNDistribution

extends AbstractDistribution
implements OrderNDistribution, Serializable

Simple base class for OrderNDistributions.

Since:
  1.2
Author:
  Samiul Hasan, Matthew Pocock, Thomas Down
See Also:
  Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.dist.Distribution
`Distribution.NullModelForwarder`

Field Summary
`protected ChangeForwarder` | `weightForwarder` The listener that will forward events from the underlying distributions to listeners for this distribution.

Fields inherited from class org.biojava.bio.dist.AbstractDistribution
`nullModelForwarder`

Fields inherited from interface org.biojava.bio.dist.Distribution
`NULL_MODEL, WEIGHTS`

Constructor Summary
`protected` | `AbstractOrderNDistribution(Alphabet alpha)` Construct a new NthOrderDistribution.

Method Summary
`Alphabet` | `getAlphabet()` The alphabet from which this spectrum emits symbols.
`protected ChangeSupport` | `getChangeSupport(ChangeType ct)` Called to retrieve the ChangeSupport for this object.
`Alphabet` | `getConditionedAlphabet()` Get the conditioned alphabet.
`Alphabet` | `getConditioningAlphabet()` Get the conditioning alphabet of this distribution.
`Distribution` | `getNullModel()` Retrieve the null model Distribution that this Distribution recognizes.
`protected double` | `getWeightImpl(AtomicSymbol sym)` Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.
`void` | `registerWithTrainer(DistributionTrainerContext dtc)` Register an IgnoreCountsTrainer instance as the trainer for this distribution.
`void` | `setNullModelImpl(Distribution nullModel)` Implement this to set the null model.
`void` | `setWeightImpl(AtomicSymbol sym, double w)` Set a weight in one of the conditioned distributions.

Methods inherited from class org.biojava.bio.dist.AbstractDistribution
`equals, getWeight, hashCode, sampleSymbol, setNullModel, setWeight`

Methods inherited from class org.biojava.utils.AbstractChangeable
`addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from class java.lang.Object
`clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait`

Methods inherited from interface org.biojava.bio.dist.OrderNDistribution
`conditionedDistributions, getDistribution, setDistribution`

Methods inherited from interface org.biojava.bio.dist.Distribution
`getWeight, sampleSymbol, setNullModel, setWeight`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Field Detail

### weightForwarder

    protected transient ChangeForwarder weightForwarder

  The listener that will forward events from the underlying distributions to listeners for this distribution.

Constructor Detail

### AbstractOrderNDistribution

    protected AbstractOrderNDistribution(Alphabet alpha)
                                  throws IllegalAlphabetException

  Construct a new NthOrderDistribution.

  Parameters:
    `alpha` - the Alpahbet this is over
  Throws:
    `IllegalAlphabetException`

Method Detail

### 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 `AbstractDistribution`

### getConditioningAlphabet

    public Alphabet getConditioningAlphabet()

  Get the conditioning alphabet of this distribution. If the `overall' alphabet is a cross-product of two alphabets, this will be the first of those alphabets. If it is a cross-product of more than two alphabets, the conditioning alphabet is the cross-product of all but the last alphabet.

  Specified by:
    `getConditioningAlphabet` in interface `OrderNDistribution`
  Returns:
    the conditioning Alphabet

### getConditionedAlphabet

    public Alphabet getConditionedAlphabet()

  Get the conditioned alphabet. This is the last alphabet in the distribution's overall cross-product. It will be the alphabet of all the sub-distributions contained within this OrderNDistribution.

  Specified by:
    `getConditionedAlphabet` in interface `OrderNDistribution`
  Returns:
    the conditioned Alphabet

### getAlphabet

    public Alphabet getAlphabet()

  Description copied from interface: `Distribution`
  The alphabet from which this spectrum emits symbols.

  Specified by:
    `getAlphabet` in interface `Distribution`
  Returns:
    the Alphabet associated with this spectrum

### getWeightImpl

    protected double getWeightImpl(AtomicSymbol sym)
                            throws IllegalSymbolException

  Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.

  Specified by:
    `getWeightImpl` in class `AbstractDistribution`
  Parameters:
    `sym` - the symbol to look up
  Returns:
    the weight
  Throws:
    `IllegalSymbolException` - if sym is not recognised

### setWeightImpl

    public void setWeightImpl(AtomicSymbol sym,
                              double w)
                       throws IllegalSymbolException,
                              ChangeVetoException

  Set a weight in one of the conditioned distributions. It is the callers responsibility to ensure that all the conditioned distributions have total weights which sum to 1.0.

  Specified by:
    `setWeightImpl` in class `AbstractDistribution`
  Parameters:
    `sym` - the symbol to set the weight for
    `w` - the new weight
  Throws:
    `IllegalSymbolException` - if the symbol is not known
    `ChangeVetoException` - if the change is to be prevented

### setNullModelImpl

    public void setNullModelImpl(Distribution nullModel)

  Description copied from class: `AbstractDistribution`
  Implement this to set the null model.

  You should not inform any change listeners in this method. All of that work has been done for you.

  Specified by:
    `setNullModelImpl` in class `AbstractDistribution`
  Parameters:
    `nullModel` - the new null model Distribution

### getNullModel

    public Distribution getNullModel()

  Description copied from interface: `Distribution`
  Retrieve the null model Distribution that this Distribution recognizes.

  Specified by:
    `getNullModel` in interface `Distribution`
  Returns:
    the apropriate null model

### registerWithTrainer

    public void registerWithTrainer(DistributionTrainerContext dtc)

  Description copied from class: `AbstractDistribution`
  Register an IgnoreCountsTrainer instance as the trainer for this distribution. Override this if you wish to implement a trainable distribution.

  Specified by:
    `registerWithTrainer` in interface `Distribution`
  Overrides:
    `registerWithTrainer` in class `AbstractDistribution`
  Parameters:
    `dtc` - the context to register with

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