## Hierarchy For Package org.biojava.bio.dp

Package Hierarchies:
  All Packages

## Class Hierarchy

- class java.lang.Object
  - class org.biojava.bio.dp.AbstractTrainer (implements org.biojava.bio.dp.TrainingAlgorithm)
    - class org.biojava.bio.dp.BaumWelchSampler (implements java.io.Serializable)
    - class org.biojava.bio.dp.BaumWelchTrainer (implements java.io.Serializable)
  - class org.biojava.bio.dp.DP
    - class org.biojava.bio.dp.PairwiseDP (implements java.io.Serializable)
  - class org.biojava.bio.dp.DP.ReverseIterator (implements java.util.Iterator, java.io.Serializable)
  - class org.biojava.bio.dp.DPFactory
  - class java.util.EventObject (implements java.io.Serializable)
    - class org.biojava.bio.dp.ModelChangeEvent
      - class org.biojava.bio.dp.TransitionEvent
  - class org.biojava.bio.dp.ModelView (implements org.biojava.bio.dp.MarkovModel)
  - class org.biojava.bio.dp.ModelView.ViewTransitionTrainer (implements java.io.Serializable, org.biojava.bio.dp.TransitionTrainer)
  - class org.biojava.bio.dp.PairDPMatrix (implements org.biojava.bio.dp.DPMatrix, java.io.Serializable)
  - class org.biojava.bio.symbol.SimpleAtomicSymbol (implements org.biojava.bio.symbol.AtomicSymbol)
    - class org.biojava.bio.dp.SimpleDotState (implements org.biojava.bio.dp.DotState, java.io.Serializable)
    - class org.biojava.bio.dp.SimpleModelInState (implements org.biojava.bio.dp.ModelInState)
  - class org.biojava.bio.dist.SimpleDistributionTrainerContext (implements org.biojava.bio.dist.DistributionTrainerContext, java.io.Serializable)
    - class org.biojava.bio.dp.SimpleModelTrainer (implements org.biojava.bio.dp.ModelTrainer, java.io.Serializable)
  - class org.biojava.bio.dp.SimpleEmissionState (implements org.biojava.bio.dp.EmissionState, java.io.Serializable)
    - class org.biojava.bio.dp.MagicalState
  - class org.biojava.bio.dp.SimpleMarkovModel (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
    - class org.biojava.bio.dp.ProfileHMM
  - class org.biojava.bio.dp.SimpleStatePath (implements java.io.Serializable, org.biojava.bio.dp.StatePath)
  - class org.biojava.bio.dp.SimpleTransitionTrainer (implements java.io.Serializable, org.biojava.bio.dp.TransitionTrainer)
  - class org.biojava.bio.dp.SimpleWeightMatrix (implements java.io.Serializable, org.biojava.bio.dp.WeightMatrix)
  - class java.lang.Throwable (implements java.io.Serializable)
    - class java.lang.Exception
      - class org.biojava.bio.BioException
        - class org.biojava.bio.dp.IllegalTransitionException
      - class org.biojava.bio.dp.ModelVetoException
  - class org.biojava.bio.dp.TrainerTransition (implements java.io.Serializable)
  - class org.biojava.bio.dp.Transition (implements java.io.Serializable)
  - class org.biojava.bio.dp.WeightMatrixAnnotator (implements org.biojava.bio.seq.SequenceAnnotator, java.io.Serializable)
  - class org.biojava.bio.dp.WMAsMM (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
  - class org.biojava.bio.dp.XmlMarkovModel

## Interface Hierarchy

- interface org.biojava.bio.Annotatable
  - interface org.biojava.bio.symbol.Symbol
    - interface org.biojava.bio.symbol.AtomicSymbol
      - interface org.biojava.bio.dp.State
        - interface org.biojava.bio.dp.DotState
        - interface org.biojava.bio.dp.EmissionState(also extends org.biojava.bio.dp.Trainable)
        - interface org.biojava.bio.dp.ModelInState(also extends org.biojava.bio.dp.Trainable)
- interface org.biojava.bio.dist.DistributionTrainerContext
  - interface org.biojava.bio.dp.ModelTrainer
- interface org.biojava.bio.dp.DPMatrix
- interface org.biojava.bio.dp.StoppingCriteria
- interface org.biojava.bio.symbol.SymbolList
  - interface org.biojava.bio.symbol.Alignment
    - interface org.biojava.bio.dp.StatePath
- interface org.biojava.bio.dp.Trainable
  - interface org.biojava.bio.dp.EmissionState(also extends org.biojava.bio.dp.State)
  - interface org.biojava.bio.dp.MarkovModel
  - interface org.biojava.bio.dp.ModelInState(also extends org.biojava.bio.dp.State)
- interface org.biojava.bio.dp.TrainingAlgorithm
- interface org.biojava.bio.dp.TransitionListener
- interface org.biojava.bio.dp.TransitionTrainer
- interface org.biojava.bio.dp.WeightMatrix