Class Hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

• tops::Alphabet
• tops::ConfigurationReader
• tops::ContextTree
• tops::ContextTreeNode
• tops::GHMMState
  • tops::GHMMExplicitDurationState
  • tops::GHMMSignalState
• tops::PhasedFactorableModelEvaluationAlgorithm
• tops::PrefixSumArray
  • tops::FactorableModelPrefixSumArray
  • tops::NullPrefixSumArray
• tops::ProbabilisticModel
  • tops::DecodableModel
    • tops::GeneralizedHiddenMarkovModel
    • tops::HiddenMarkovModel
  • tops::FactorableModel
    • tops::DiscreteIIDModel
      • tops::DegenerateDistribution
    • tops::VariableLengthMarkovChain
  • tops::InhomogeneousFactorableModel
    • tops::InhomogeneousMarkovChain
  • tops::MaximumDependenceDecomposition
  • tops::MultipleSequentialModel
  • tops::PairDecodableModel
  • tops::ProbabilisticModelDecorator
    • tops::FixedSequenceAtPosition
    • tops::PhasedRunLengthDistribution
  • tops::SimilarityBasedSequenceWeighting
  • tops::TargetModel
  • tops::UniformGCModel
• tops::ProbabilisticModelCreator
  • tops::AkaikeInformationCriteria
  • tops::BayesianInformationCriteria
  • tops::BernoulliModelCreator
  • tops::DiscreteIIDModelCreator
  • tops::GeneralizedHiddenMarkovModelCreator
  • tops::HiddenMarkovModelCreator
  • tops::InhomogeneousMarkovChainCreator
  • tops::MultipleSequentialModelCreator
  • tops::PairHiddenMarkovModelCreator
  • tops::SimilarityBasedSequenceWeightingCreator
  • tops::SmoothedHistogramBurge
  • tops::SmoothedHistogramKernelDensity
  • tops::SmoothedHistogramStanke
  • tops::TargetModelCreator
  • tops::TrainDiscreteIIDModel
  • tops::TrainFixedLengthMarkovChain
  • tops::TrainGHMMTransitionsCreator
  • tops::TrainHMMBaumWelch
  • tops::TrainInterpolatedMarkovChain
  • tops::TrainInterpolatedPhasedMarkovChain
  • tops::TrainPhasedMarkovChain
  • tops::TrainPhasedMarkovChainContextAlgorithm
  • tops::TrainPHMMBaumWelch
  • tops::TrainSimilarityBasedSequenceWeighting
  • tops::TrainVariableLengthInhomogeneousMarkovChain
  • tops::TrainVariableLengthMarkovChain
  • tops::TrainWeightArrayModel
  • tops::VariableLengthMarkovChainCreator
• tops::ProbabilisticModelCreatorClient
• tops::ProbabilisticModelParameters
• tops::ProbabilisticModelParameterValue
  • tops::DoubleMapParameterValue
  • tops::DoubleParameterValue
  • tops::DoubleVectorParameterValue
  • tops::IntParameterValue
  • tops::IntVectorParameterValue
  • tops::StringMapParameterValue
  • tops::StringParameterValue
  • tops::StringVectorParameterValue
• tops::SequenceEntry
• tops::SequenceFactory
• tops::SequenceFormat
  • tops::FastaSequenceFormat
• tops::SequenceFormatManager
• tops::Symbol