Uses of Package
de.jstacs

Packages that use de.jstacs
de.jstacs This package is the root package for the most and important packages. 
de.jstacs.algorithms.optimization.termination   
de.jstacs.classifier This package provides the framework for any classifier. 
de.jstacs.classifier.assessment This package allows to assess classifiers. 
de.jstacs.classifier.modelBased Provides the classes for Classifiers that are based on Model
de.jstacs.classifier.scoringFunctionBased Provides the classes for Classifiers that are based on ScoringFunctions. 
de.jstacs.classifier.scoringFunctionBased.gendismix Provides an implementation of a classifier that allows to train the parameters of a set of NormalizableScoringFunctions by a unified generative-discriminative learning principle 
de.jstacs.classifier.scoringFunctionBased.logPrior Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors 
de.jstacs.classifier.scoringFunctionBased.msp Provides an implementation of a classifier that allows to train the parameters of a set of ScoringFunctions either by maximum supervised posterior (MSP) or by maximum conditional likelihood (MCL) 
de.jstacs.classifier.scoringFunctionBased.sampling Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingScoringFunctions and that sample parameters using the Metropolis-Hastings algorithm. 
de.jstacs.data Provides classes for the representation of data. 
de.jstacs.data.alphabets Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences 
de.jstacs.data.bioJava Provides an adapter between the representation of data in BioJava and the representation used in Jstacs. 
de.jstacs.data.sequences Provides classes for representing sequences. 
de.jstacs.data.sequences.annotation Provides the facilities to annotate Sequences using a number of pre-defined annotation types, or additional implementations of the SequenceAnnotation class 
de.jstacs.io Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and Storables to an XML-representation 
de.jstacs.models Provides the interface Model and its abstract implementation AbstractModel, which is the super class of all other models. 
de.jstacs.models.discrete   
de.jstacs.models.discrete.homogeneous   
de.jstacs.models.discrete.homogeneous.parameters   
de.jstacs.models.discrete.inhomogeneous This package contains various inhomogeneous models. 
de.jstacs.models.discrete.inhomogeneous.parameters   
de.jstacs.models.discrete.inhomogeneous.shared   
de.jstacs.models.hmm The package provides all interfaces and classes for a hidden Markov model (HMM). 
de.jstacs.models.hmm.models The package provides different implementations of hidden Markov models based on AbstractHMM 
de.jstacs.models.hmm.states.emissions   
de.jstacs.models.hmm.states.emissions.continuous   
de.jstacs.models.hmm.states.emissions.discrete   
de.jstacs.models.hmm.training The package provides all classes used to determine the training algorithm of a hidden Markov model 
de.jstacs.models.hmm.transitions The package provides all interfaces and classes for transitions used in hidden Markov models. 
de.jstacs.models.hmm.transitions.elements   
de.jstacs.models.mixture This package is the super package for any mixture model. 
de.jstacs.models.mixture.motif   
de.jstacs.models.mixture.motif.positionprior   
de.jstacs.models.phylo   
de.jstacs.models.phylo.parser   
de.jstacs.models.utils   
de.jstacs.motifDiscovery This package provides the framework including the interface for any de novo motif discoverer 
de.jstacs.motifDiscovery.history   
de.jstacs.parameters This package provides classes for parameters that establish a general convention for the description of parameters as defined in the Parameter-interface. 
de.jstacs.parameters.validation Provides classes for the validation of Parameter values 
de.jstacs.results This package provides classes for results and sets of results. 
de.jstacs.sampling This package contains many classes that can be used while a sampling. 
de.jstacs.scoringFunctions Provides ScoringFunctions that can be used in a ScoreClassifier
de.jstacs.scoringFunctions.directedGraphicalModels Provides ScoringFunctions that are equivalent to directed graphical models. 
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures Provides the facilities to learn the structure of a BayesianNetworkScoringFunction
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures Provides the facilities to learn the structure of a BayesianNetworkScoringFunction as a Bayesian tree using a number of measures to define a rating of structures 
de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures Provides the facilities to learn the structure of a BayesianNetworkScoringFunction as a permuted Markov model using a number of measures to define a rating of structures 
de.jstacs.scoringFunctions.homogeneous Provides ScoringFunctions that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence 
de.jstacs.scoringFunctions.mix Provides ScoringFunctions that are mixtures of other ScoringFunctions. 
de.jstacs.scoringFunctions.mix.motifSearch   
de.jstacs.utils This package contains a bundle of useful classes and interfaces like ... 
de.jstacs.utils.galaxy   
 

Classes in de.jstacs used by de.jstacs
DataType
          This enum defines a number of data types that can be used for Parameters and Result s.
 

Classes in de.jstacs used by de.jstacs.algorithms.optimization.termination
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.classifier
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.classifier.assessment
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.classifier.modelBased
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.gendismix
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.logPrior
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.msp
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.sampling
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.data
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.data.alphabets
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.data.bioJava
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.data.sequences
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.data.sequences.annotation
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.io
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
 

Classes in de.jstacs used by de.jstacs.models
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.models.discrete
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.models.discrete.homogeneous
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.models.discrete.homogeneous.parameters
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous.parameters
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous.shared
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.models.hmm
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.models.hmm.models
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.models.hmm.states.emissions
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.hmm.states.emissions.continuous
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.hmm.states.emissions.discrete
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.hmm.training
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.hmm.transitions
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.hmm.transitions.elements
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.mixture
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.models.mixture.motif
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.models.mixture.motif.positionprior
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.phylo
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.models.phylo.parser
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
 

Classes in de.jstacs used by de.jstacs.models.utils
NotTrainedException
          A NotTrainedException is thrown if the user tries to use an untrained model.
 

Classes in de.jstacs used by de.jstacs.motifDiscovery
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.motifDiscovery.history
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.parameters
DataType
          This enum defines a number of data types that can be used for Parameters and Result s.
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.parameters.validation
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.results
DataType
          This enum defines a number of data types that can be used for Parameters and Result s.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.sampling
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.scoringFunctions
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.scoringFunctions.homogeneous
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.scoringFunctions.mix
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.scoringFunctions.mix.motifSearch
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
WrongAlphabetException
          A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.
 

Classes in de.jstacs used by de.jstacs.utils
InstantiableFromParameterSet
          Interface for all classes that can be instantiated from a InstanceParameterSet.
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.
 

Classes in de.jstacs used by de.jstacs.utils.galaxy
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
Storable
          This is the root interface for all immutable objects that must be stored in e.g. a file or a database.