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.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.cll Provides the implementation of the log conditional likelihood as an OptimizableFunction and a classifier that uses log conditional likelihood or supervised posterior to learn the parameters of a set of ScoringFunctions 
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.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.mixture This package is the super package for any mixture model. 
de.jstacs.models.mixture.gibbssampling This package contains many classes that can be used while a Gibbs sampling. 
de.jstacs.models.mixture.motif   
de.jstacs.models.mixture.motif.positionprior   
de.jstacs.models.utils   
de.jstacs.motifDiscovery This package provides the framework including the interface for any de novo motif discoverer 
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.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 ... 
 

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.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.
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.scoringFunctionBased.cll
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.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.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.
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
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.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.gibbssampling
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.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.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.
 

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.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.
 

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.
 

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.