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

Package Hierarchies:
  All Packages

## Class Hierarchy

- java.lang.Object
  - org.biojava.utils.AbstractChangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.symbol.AbstractSymbol (implements org.biojava.bio.symbol.Symbol)
      - org.biojava.bio.symbol.FundamentalAtomicSymbol (implements org.biojava.bio.symbol.AtomicSymbol, java.io.Serializable)
        - org.biojava.bio.dp.SimpleDotState (implements org.biojava.bio.dp.DotState, java.io.Serializable)
        - org.biojava.bio.dp.SimpleModelInState (implements org.biojava.bio.dp.ModelInState)
    - org.biojava.bio.dp.SimpleEmissionState (implements org.biojava.bio.dp.EmissionState, java.io.Serializable)
      - org.biojava.bio.dp.MagicalState
    - org.biojava.bio.dp.SimpleMarkovModel (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
      - org.biojava.bio.dp.ProfileHMM
    - org.biojava.bio.dp.WMAsMM (implements org.biojava.bio.dp.MarkovModel, java.io.Serializable)
  - org.biojava.bio.dp.AbstractTrainer (implements org.biojava.bio.dp.TrainingAlgorithm)
    - org.biojava.bio.dp.BaumWelchSampler (implements java.io.Serializable)
    - org.biojava.bio.dp.BaumWelchTrainer (implements java.io.Serializable)
  - org.biojava.bio.dp.BackPointer
  - org.biojava.bio.dp.DP
  - org.biojava.bio.dp.DP.ReverseIterator (implements java.util.Iterator<E>, java.io.Serializable)
  - org.biojava.bio.dp.DPFactory.DefaultFactory (implements org.biojava.bio.dp.DPFactory)
  - org.biojava.bio.dp.ScoreType.NullModel (implements org.biojava.bio.dp.ScoreType, java.io.Serializable)
  - org.biojava.bio.dp.ScoreType.Odds (implements org.biojava.bio.dp.ScoreType, java.io.Serializable)
  - org.biojava.bio.dp.ScoreType.Probability (implements org.biojava.bio.dp.ScoreType, java.io.Serializable)
  - org.biojava.bio.dist.SimpleDistributionTrainerContext (implements org.biojava.bio.dist.DistributionTrainerContext, java.io.Serializable)
    - org.biojava.bio.dp.SimpleModelTrainer (implements org.biojava.bio.dp.ModelTrainer, java.io.Serializable)
  - org.biojava.bio.dp.SimpleHMMTrainer (implements org.biojava.bio.dp.HMMTrainer)
  - org.biojava.bio.dp.SimpleWeightMatrix (implements java.io.Serializable, org.biojava.bio.dp.WeightMatrix)
  - java.lang.Throwable (implements java.io.Serializable)
    - java.lang.Exception
      - org.biojava.bio.BioException
        - org.biojava.bio.dp.IllegalTransitionException
  - org.biojava.bio.dp.TrainerTransition (implements java.io.Serializable)
  - org.biojava.bio.dp.Transition (implements java.io.Serializable)
  - org.biojava.utils.Unchangeable (implements org.biojava.utils.Changeable)
    - org.biojava.bio.dp.SimpleStatePath (implements java.io.Serializable, org.biojava.bio.dp.StatePath)
  - org.biojava.bio.dp.WeightMatrixAnnotator (implements org.biojava.bio.seq.SequenceAnnotator, java.io.Serializable)
  - org.biojava.bio.dp.XmlMarkovModel

## Interface Hierarchy

- org.biojava.utils.Changeable
  - org.biojava.bio.Annotatable
    - org.biojava.bio.symbol.Symbol
      - org.biojava.bio.symbol.BasisSymbol
        - org.biojava.bio.symbol.AtomicSymbol
          - org.biojava.bio.dp.State
            - org.biojava.bio.dp.DotState
            - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.Trainable)
            - org.biojava.bio.dp.ModelInState
  - org.biojava.bio.dp.EmissionState (also extends org.biojava.bio.dp.State, org.biojava.bio.dp.Trainable)
  - org.biojava.bio.dp.MarkovModel
  - org.biojava.bio.symbol.SymbolList
    - org.biojava.bio.symbol.Alignment
      - org.biojava.bio.dp.StatePath
- org.biojava.bio.dist.DistributionTrainerContext
  - org.biojava.bio.dp.ModelTrainer
- org.biojava.bio.dp.DPFactory
- org.biojava.bio.dp.DPMatrix
- org.biojava.bio.dp.HMMTrainer
- org.biojava.bio.dp.ScoreType
- org.biojava.bio.dp.StoppingCriteria
- org.biojava.bio.dp.Trainable
  - org.biojava.bio.dp.EmissionState (also extends org.biojava.utils.Changeable, org.biojava.bio.dp.State)
- org.biojava.bio.dp.TrainingAlgorithm
- org.biojava.bio.dp.TransitionTrainer
- org.biojava.bio.dp.WeightMatrix