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AbstractTrainer (biojava-legacy 1.9.5 API)

  • java.lang.Object
    • org.biojava.bio.dp.AbstractTrainer
  • All Implemented Interfaces:
    TrainingAlgorithm
    Direct Known Subclasses:
    BaumWelchSampler, BaumWelchTrainer
    public abstract class AbstractTrainer
extends Object
implements TrainingAlgorithm

    An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.

    Author:
    Matthew Pocock, Thomas Down

    • Constructor Summary

      Constructors 
      Modifier Constructor Description
      protected AbstractTrainer()  
        AbstractTrainer​(DP dp)  

    • Method Summary

      All Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      double getCurrentScore()  
      int getCycle()  
      DP getDP()  
      double getLastScore()  
      protected abstract double singleSequenceIteration​(ModelTrainer trainer, SymbolList symList)  
      void train​(SequenceDB db, double nullModelWeight, StoppingCriteria stopper)

      Trains the sequences in db until stopper says to finnish.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • AbstractTrainer

        public AbstractTrainer​(DP dp)

      • AbstractTrainer

        protected AbstractTrainer()

    • Method Detail

      • getLastScore

        public double getLastScore()
        Specified by:
        getLastScore in interface TrainingAlgorithm

      • getCurrentScore

        public double getCurrentScore()
        Specified by:
        getCurrentScore in interface TrainingAlgorithm

      • getCycle

        public int getCycle()
        Specified by:
        getCycle in interface TrainingAlgorithm

      • getDP

        public DP getDP()
        Specified by:
        getDP in interface TrainingAlgorithm

      • singleSequenceIteration

        protected abstract double singleSequenceIteration​(ModelTrainer trainer,
                                                  SymbolList symList)
                                           throws IllegalSymbolException,
                                                  IllegalTransitionException,
                                                  IllegalAlphabetException
        Throws:
        IllegalSymbolException
        IllegalTransitionException
        IllegalAlphabetException

      • train

        public void train​(SequenceDB db,
                  double nullModelWeight,
                  StoppingCriteria stopper)
           throws IllegalSymbolException,
                  BioException

        Trains the sequences in db until stopper says to finnish.

        Specified by:
        train in interface TrainingAlgorithm
        Throws:
        IllegalSymbolException
        BioException