Package org.biojava.bio.dist

Class TranslatedDistribution

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.dist.TranslatedDistribution
All Implemented Interfaces:
Serializable, Distribution, Changeable
public class TranslatedDistribution extends AbstractChangeable implements Distribution, Serializable
A translated view of some underlying distribution. The getWeight method returns the result of calling getWeight on the underlying distribution, having first translated the Symbol parameter using the supplied ReversibleTranslationTable. All changes to the underlying distribution are reflected by the TranslatedDistribution.

The TranslatedDistribution is not directly mutable: calling setWeight will result in a ChangeVetoException. However, a DistributionTrainer may be registered for a TranslatedDistribution. Any counts received by this trainer are untranslated then forwarded to the underlying distribution. It is valid to add counts to both a TranslatedDistribution and its underlying distribution in a single training session, so TranslatedDistribution objects are useful for tying parameters together when training Markov Models.

Example usage

 Distribution d = DistributionFactory.DEFAULT.createDistribution(DNATools.getDNA());
 d.setWeight(DNATools.a(), 0.7);
 d.setWeight(DNATools.c(), 0.1);
 d.setWeight(DNATools.g(), 0.1);
 d.setWeight(DNATools.t(), 0.1);
 Distribution complemented = new TranslatedDistribution(
     DNATools.complementTable(),
     d,
     DistributionFactory.DEFAULT
 );
 System.out.println(
    "complemented.getWeight(DNATools.t()) = " +
    complemented.getWeight(DNATools.t())
 );  // Should print 0.7
Since:
1.1
Author:
Matthew Pocock, Thomas Down
See Also:

  • Constructor Details

  • Method Details

    • 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

    • getWeight

      public double getWeight(Symbol sym) throws IllegalSymbolException
      Description copied from interface: Distribution

      Return the probability that Symbol s is emitted by this spectrum.

      If the symbol is ambiguou, then it is the sum of the probability that each one of the matching symbols was emitted.

      Specified by:
      getWeight in interface Distribution
      Parameters:
      sym - the Symbol emitted
      Returns:
      the probability of emitting that symbol
      Throws:
      IllegalSymbolException - if s is not from this state's alphabet

    • setWeight

      public void setWeight(Symbol sym, double weight) throws IllegalSymbolException, ChangeVetoException
      Description copied from interface: Distribution
      Set the probability or odds that Symbol s is emitted by this state.
      Specified by:
      setWeight in interface Distribution
      Parameters:
      sym - the Symbol emitted
      weight - the probability of emitting that symbol
      Throws:
      IllegalSymbolException - if s is not from this state's alphabet, or if it is an ambiguity symbol and the implementation can't handle this case
      ChangeVetoException - if this state does not allow weights to be tampered with, or if one of the listeners vetoed this change

    • sampleSymbol

      public Symbol sampleSymbol()
      Description copied from interface: Distribution
      Sample a symbol from this state's probability distribution.
      Specified by:
      sampleSymbol in interface Distribution
      Returns:
      the symbol sampled

    • 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

    • setNullModel

      public void setNullModel(Distribution dist) throws IllegalAlphabetException, ChangeVetoException
      Description copied from interface: Distribution
      Set the null model Distribution that this Distribution recognizes.
      Specified by:
      setNullModel in interface Distribution
      Parameters:
      dist - the new null model Distribution
      Throws:
      IllegalAlphabetException - if the null model has the wrong alphabet
      ChangeVetoException - if this Distirbution doesn't support setting the null model, or if one of its listeners objects

    • getTable

      public ReversibleTranslationTable getTable()
      Retrieve the translation table encapsulating the map from this emission spectrum to the underlying one.
      Returns:
      a ReversibleTranslationtTable

    • registerWithTrainer

      public void registerWithTrainer(DistributionTrainerContext dtc)
      Description copied from interface: Distribution

      Register this distribution with a training context.

      This should be invoked from within dtc.addDistribution(). This method is responsible for constructing a suitable DistributionTrainer instance and registering it by calling dtc.registerDistributionTrainer(this, trainer). If the distribution is a view onto another distribution, it can force the other to be registered by calling dtc.addDistribution(other), and can then get on with registering it's own trainer.

      Specified by:
      registerWithTrainer in interface Distribution
      Parameters:
      dtc - the DistributionTrainerContext with witch to register a trainer

    • 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