tops::AkaikeInformationCriteria | This class implements the Akaike Information Criteria |
tops::Alphabet | A class representing Alphabet |
tops::BayesianInformationCriteria | Bayesian Information Criteria |
tops::BernoulliModelCreator | This class is a factory for the bernoulli distribution |
tops::ConfigurationReader | This class reads a configuration file |
tops::ContextTree | This class represents a context tree |
tops::ContextTreeNode | This is a context tree node |
tops::DecodableModel | Interface defining probabilistic model with the viterbi, forward and backward algorithm |
tops::DegenerateDistribution | A probabilistic model that emits a constant integer value |
tops::DiscreteIIDModel | This represent probability distributions over a finite set of symbols |
tops::DiscreteIIDModelCreator | This class is a factory for the finite discrete distribution |
tops::DoubleMapParameterValue | Probability table |
tops::DoubleParameterValue | Double parameter value |
tops::DoubleVectorParameterValue | Double vector parameter value |
tops::FactorableModel | Abstract class defining models in which the likelihood of the sequence is factorable in the sense that they can be expressed as a product of terms evaluated at each position in a sequence |
tops::FactorableModelPrefixSumArray | This class provides an interface for working with the prefix sum arrays |
tops::FastaSequenceFormat | Fasta Format |
tops::FixedSequenceAtPosition | A decorator that forces the emission of the same sequence at a fixed position of the sequence |
tops::GeneralizedHiddenMarkovModel | This is a class representing Hidden semi-Markov Models |
tops::GeneralizedHiddenMarkovModelCreator | This class is a factory for the finite discrete distribution |
tops::GHMMExplicitDurationState | GHMM Explicit duration state |
tops::GHMMSignalState | GHMM signal states |
tops::GHMMState | Represents a GHMM State |
tops::HiddenMarkovModel | This class represents a hidden markov model |
tops::HiddenMarkovModelCreator | This class is a factory for the finite discrete distribution |
tops::InhomogeneousFactorableModel | Interface defining inhomogeneous models in which the likelihood of the sequence is factorable in the sense that they can be expressed as a product of terms evaluated at each position in a sequence |
tops::InhomogeneousMarkovChain | Inhomogeneous Markov chain |
tops::InhomogeneousMarkovChainCreator | This class is a factory for the variable length markov chain |
tops::IntParameterValue | Integer parameter value |
tops::IntVectorParameterValue | Integer vector parameter value |
tops::MaximumDependenceDecomposition | Maximum Dependence Decomposition: not implemented yet |
tops::MultipleSequentialModel | This class is a model that concatenates multiple models |
tops::MultipleSequentialModelCreator | This class is a factory for the Target Model |
tops::NullPrefixSumArray | This class is a generic prefix sum array |
tops::PairDecodableModel | Interface defining probabilistic model with the viterbi, forward and backward algorithm for pairs of sequences |
tops::PairHiddenMarkovModelCreator | This class is a factory for the finite discrete distribution |
tops::PhasedFactorableModelEvaluationAlgorithm | Evaluation algorithm for factorable models |
tops::PhasedRunLengthDistribution | Provides mechanisms to control the phase of a probabilistic model |
tops::PrefixSumArray | This class provides an interface for working with the prefix sum arrays |
tops::ProbabilisticModel | This is an abstract class representing a generative probabilistic model |
tops::ProbabilisticModelCreator | Represents an algorithm to create a probabilistic model |
tops::ProbabilisticModelCreatorClient | Creates a new probabilistic model |
tops::ProbabilisticModelDecorator | Decorator for the probabilistic model |
tops::ProbabilisticModelParameters | This class registers a set of parameters |
tops::ProbabilisticModelParameterValue | Represents a parameter value |
tops::SequenceEntry | Represent a sequence entry |
tops::SequenceFactory | Provides factory methods for creating objects of type Sequence |
tops::SequenceFormat | Represents a format for the sequence |
tops::SequenceFormatManager | Sequence Format Manager |
tops::SimilarityBasedSequenceWeighting | This class is the implementation of Similiarity Based Sequence Weighting |
tops::SimilarityBasedSequenceWeightingCreator | This class is a factory for the Target Model |
tops::SmoothedHistogramBurge | Creates a smoothed histogram using Burge algorithm |
tops::SmoothedHistogramKernelDensity | Estimates a smoothed histogram using kernel density estimation |
tops::SmoothedHistogramStanke | Use this to create a smoothed histogram |
tops::StringMapParameterValue | String vector parameter value |
tops::StringParameterValue | String parameter value |
tops::StringVectorParameterValue | String vector parameter value |
tops::Symbol | This class represents a symbol |
tops::TargetModel | This class is the Target Model |
tops::TargetModelCreator | This class is a factory for the Target Model |
tops::TrainDiscreteIIDModel | Creates a Multinomial Distribution |
tops::TrainFixedLengthMarkovChain | Creates a fixed length markov chain |
tops::TrainGHMMTransitionsCreator | This class is a factory for the Multinomial Distribution |
tops::TrainHMMBaumWelch | Creates a HMM using Baum-Welch |
tops::TrainInterpolatedMarkovChain | Creates a fixed length markov chain |
tops::TrainInterpolatedPhasedMarkovChain | Train a InterpolatedPhased Markov Chain |
tops::TrainPhasedMarkovChain | Train a Phased Markov Chain |
tops::TrainPhasedMarkovChainContextAlgorithm | Train a Phased Markov Chain using the Context Algorithm |
tops::TrainPHMMBaumWelch | Creates a HMM using Baum-Welch |
tops::TrainSimilarityBasedSequenceWeighting | Creates a similarity based sequence weighting model |
tops::TrainVariableLengthInhomogeneousMarkovChain | Train a inhomogeneous VLMC |
tops::TrainVariableLengthMarkovChain | This class trains the Variable Length Markov Chain using the context algorithm |
tops::TrainWeightArrayModel | A creator that trains a Weight Array Model |
tops::UniformGCModel | This class is the Target Model |
tops::VariableLengthMarkovChain | This class is a Variable Length Markov Chain |
tops::VariableLengthMarkovChainCreator | This class is a factory for the variable length markov chain |