org.biojava.bio.dp

Interfaces

• DotState
• DPFactory
• DPMatrix
• EmissionState
• HMMTrainer
• MarkovModel
• ModelInState
• ModelTrainer
• ScoreType
• State
• StatePath
• StoppingCriteria
• Trainable
• TrainingAlgorithm
• TransitionTrainer
• WeightMatrix

Classes

• AbstractTrainer
• BackPointer
• BaumWelchSampler
• BaumWelchTrainer
• DP
• DP.ReverseIterator
• DPFactory.DefaultFactory
• MagicalState
• ProfileHMM
• ScoreType.NullModel
• ScoreType.Odds
• ScoreType.Probability
• SimpleDotState
• SimpleEmissionState
• SimpleHMMTrainer
• SimpleMarkovModel
• SimpleModelInState
• SimpleModelTrainer
• SimpleStatePath
• SimpleWeightMatrix
• TrainerTransition
• Transition
• WeightMatrixAnnotator
• WMAsMM
• XmlMarkovModel

Exceptions

• IllegalTransitionException