Home Original page

SimpleDistributionTrainer (biojava-legacy 1.9.5 API)

  • java.lang.Object
    • org.biojava.bio.dist.SimpleDistributionTrainer
  • All Implemented Interfaces:
    Serializable, DistributionTrainer
    public final class SimpleDistributionTrainer
extends Object
implements DistributionTrainer, Serializable

    A simple implemenation of a distribution trainer.

    This requires the distribuiton being trained to have a working setWeight method that doesn't throw an UnsupportedOperationExcepiton.

    Author:
    Matthew Pocock
    See Also:
    Serialized Form

    • Constructor Summary

      Constructors 
      Constructor Description
      SimpleDistributionTrainer​(Distribution dis)

      Deprecated.

       

    • Method Summary

      All Methods Instance Methods Concrete Methods Deprecated Methods 
      Modifier and Type Method Description
      void addCount​(DistributionTrainerContext dtc, AtomicSymbol sym, double count)

      Deprecated.

      Registers that sym was counted in this state.
      void clearCounts​(DistributionTrainerContext dtc)

      Deprecated.

      Clears all of the counts to zero.
      double getCount​(DistributionTrainerContext dtc, AtomicSymbol sym)

      Deprecated.

      Get the current count for this state.
      void train​(DistributionTrainerContext dtc, double weight)

      Deprecated.

      Trains the Distribution, given a null model.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • SimpleDistributionTrainer

        public SimpleDistributionTrainer​(Distribution dis)
                          throws IllegalAlphabetException

        Deprecated.

        Throws:
        IllegalAlphabetException

    • Method Detail

      • addCount

        public void addCount​(DistributionTrainerContext dtc,
                     AtomicSymbol sym,
                     double count)
              throws IllegalSymbolException

        Deprecated.

        Registers that sym was counted in this state.

        This method may be called multiple times with the same symbol. In this case, the times should be summed.

        Specified by:
        addCount in interface DistributionTrainer
        Parameters:
        dtc - the DistributionTrainerContext within which the count was added
        sym - the Symbol seen
        count - the number of times to add
        Throws:
        IllegalSymbolException - if sym is not recognised

      • getCount

        public double getCount​(DistributionTrainerContext dtc,
                       AtomicSymbol sym)
                throws IllegalSymbolException

        Deprecated.

        Get the current count for this state.

        This method may be called multiple times with the same symbol. Each time it should return the agregate of the counts added with addCount since the last invocation of clearCounts.

        Specified by:
        getCount in interface DistributionTrainer
        Parameters:
        dtc - the DistributionTrainerContext within which the count was added
        sym - the Symbol seen
        Returns:
        the agregate of the counts
        Throws:
        IllegalSymbolException - if sym is not recognised

      • train

        public void train​(DistributionTrainerContext dtc,
                  double weight)
           throws ChangeVetoException

        Deprecated.

        Trains the Distribution, given a null model.

        This will use the information collected with multiple addCount calls, and the null model to generate the new weights.

        This method should not modify the underlying counts.

        Specified by:
        train in interface DistributionTrainer
        Parameters:
        dtc - the context to use
        weight - how many lots of the null model to add
        Throws:
        ChangeVetoException - if the distribution could not have its weights modified

      • clearCounts

        public void clearCounts​(DistributionTrainerContext dtc)

        Deprecated.

        Clears all of the counts to zero.

        Specified by:
        clearCounts in interface DistributionTrainer