Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD

## org.biojava.bio.dist
Class UniformDistribution

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

All Implemented Interfaces:
  Serializable, Distribution, Changeable

    public class UniformDistribution

extends AbstractDistribution
implements Serializable

An implementation of an uniform distribution

Since:
  1.0
Author:
  Matthew Pocock, Mark Schreiber, Thomas Down
See Also:
  Serialized Form

Nested Class Summary

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

Field Summary

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

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

Constructor Summary
`UniformDistribution(FiniteAlphabet alphabet)` Create a new UniformDistribution.

Method Summary
`Alphabet` | `getAlphabet()` The alphabet from which this spectrum emits symbols.
`Distribution` | `getNullModel()` Retrieve the null model Distribution that this Distribution recognizes.
`protected double` | `getWeightImpl(AtomicSymbol s)` Override this method to implement getting the weight for an atomic symbol.
`void` | `registerWithTrainer(DistributionTrainerContext dtc)` Register an IgnoreCountsTrainer instance as the trainer for this distribution.
`protected void` | `setNullModelImpl(Distribution nullModel)` Assign a background distribution.
`protected void` | `setWeightImpl(AtomicSymbol sym, double weight)` Implement this to actually set the weight.

Methods inherited from class org.biojava.bio.dist.AbstractDistribution
`equals, getChangeSupport, 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.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Constructor Detail

### UniformDistribution

    public UniformDistribution(FiniteAlphabet alphabet)

  Create a new UniformDistribution.

  Parameters:
    `alphabet` - the finite alphabet to be over

Method Detail

### 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

### 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

### setNullModelImpl

    protected void setNullModelImpl(Distribution nullModel)
                             throws IllegalAlphabetException

  Assign a background distribution.

  Specified by:
    `setNullModelImpl` in class `AbstractDistribution`
  Parameters:
    `nullModel` - the background distribution to assign
  Throws:
    `IllegalAlphabetException` - if nullModel is over an incompattible alphabet

### getWeightImpl

    protected double getWeightImpl(AtomicSymbol s)
                            throws IllegalSymbolException

  Description copied from class: `AbstractDistribution`
  Override this method to implement getting the weight for an atomic symbol. You should just do what is necessary to fetch state. All the work with exceptions and listeners will have been handled for you.

  Specified by:
    `getWeightImpl` in class `AbstractDistribution`
  Parameters:
    `s` - the AtomicSymbol to get the weight for
  Returns:
    the weight
  Throws:
    `IllegalSymbolException` - if sym is not known

### setWeightImpl

    protected void setWeightImpl(AtomicSymbol sym,
                                 double weight)
                          throws ChangeVetoException

  Description copied from class: `AbstractDistribution`
  Implement this to actually set the weight.

  Do not inform any listeners. This has already been done for you. Just update state.

  Specified by:
    `setWeightImpl` in class `AbstractDistribution`
  Parameters:
    `sym` - the AtomicSymbol to update for
    `weight` - the new weight for that symbol
  Throws:
    `ChangeVetoException` - if the change is to be prevented

### 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

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD