Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

## 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 `Classifier`s that are based on `Model`s
de.jstacs.classifier.scoringFunctionBased | Provides the classes for `Classifier`s that are based on `ScoringFunction`s.
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 `Sequence`s 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 `Storable`s 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 `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.directedGraphicalModels | Provides `ScoringFunction`s 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 `ScoringFunction`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.
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 datatypes that can be used for `Parameter` and `Result`.

Classes in de.jstacs used by de.jstacs.classifier
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.classifier.modelBased
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.cll
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.logPrior
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.data.alphabets
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.data.bioJava
WrongAlphabetException A WrongAlphabetException is thrown if a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.data.sequences
WrongAlphabetException A WrongAlphabetException is thrown if a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.data.sequences.annotation
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.models.discrete
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

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 NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.models.discrete.homogeneous.parameters
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous.parameters
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.models.mixture
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

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 NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 a data file did not match the given alphabet.

Classes in de.jstacs used by de.jstacs.models.mixture.motif.positionprior
NonParsableException A NonParsable exception is thrown if some object could not be restored 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.
WrongAlphabetException A WrongAlphabetException is thrown if a data file did not match the given alphabet.

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 datatypes that can be used for `Parameter` and `Result`.
InstantiableFromParameterSet Interface for all classes that can be instantiated from a `InstanceParameterSet`.
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 datatypes that can be used for `Parameter` and `Result`.
NonParsableException A NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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 NonParsable exception is thrown if some object could not be restored 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.

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES