Package org.biojava.bio.dist

Class 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:
    Serialized Form

    • Method Detail

      • 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

      • 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