Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

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