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## Uses of Package
de.jstacs.io

Packages that use de.jstacs.io
de.jstacs | This package is the root package for the most and important packages.
de.jstacs.algorithms.optimization.termination | Provides classes for termination conditions that can be used in algorithms
de.jstacs.classifiers | This package provides the framework for any classifier.
de.jstacs.classifiers.assessment | This package allows to assess classifiers.
de.jstacs.classifiers.differentiableSequenceScoreBased | Provides the classes for `Classifier`s that are based on `SequenceScore`s.
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix | Provides an implementation of a classifier that allows to train the parameters of a set of `DifferentiableStatisticalModel`s by a unified generative-discriminative learning principle
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior | Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors
de.jstacs.classifiers.differentiableSequenceScoreBased.msp | Provides an implementation of a classifier that allows to train the parameters of a set of `DifferentiableStatisticalModel`s either by maximum supervised posterior (MSP) or by maximum conditional likelihood (MCL)
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling | Provides the classes for `AbstractScoreBasedClassifier`s that are based on `SamplingDifferentiableStatisticalModel`s and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.classifiers.performanceMeasures | This package provides the implementations of performance measures that can be used to assess any classifier
de.jstacs.classifiers.trainSMBased | Provides the classes for `Classifier`s that are based on `TrainableStatisticalModel`s
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.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.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.sequenceScores.differentiable |
de.jstacs.sequenceScores.differentiable.logistic |
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | Provides `DifferentiableStatisticalModel`s that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures | Provides the facilities to learn the structure of a `BayesianNetworkDiffSM`.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures | Provides the facilities to learn the structure of a `BayesianNetworkDiffSM` as a Bayesian tree using a number of measures to define a rating of structures
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures | Provides the facilities to learn the structure of a `BayesianNetworkDiffSM` as a permuted Markov model using a number of measures to define a rating of structures
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous | Provides `DifferentiableStatisticalModel`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
de.jstacs.sequenceScores.statisticalModels.trainable | Provides all `TrainableStatisticalModel`s, which can be learned from a single `DataSet`.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous | This package contains various inhomogeneous models.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm | The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models | The package provides different implementations of hidden Markov models based on `AbstractHMM`
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete |
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training | The package provides all classes used to determine the training algorithm of a hidden Markov model
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions | The package provides all interfaces and classes for transitions used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture | This package is the super package for any mixture model.
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior |
de.jstacs.sequenceScores.statisticalModels.trainable.phylo |
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ...
de.jstacs.utils.galaxy |

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

Classes in de.jstacs.io used by de.jstacs.algorithms.optimization.termination
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

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

Classes in de.jstacs.io used by de.jstacs.classifiers.assessment
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
ParameterSetParser.NotInstantiableException An `Exception` that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased.msp
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased.sampling
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.classifiers.performanceMeasures
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.classifiers.trainSMBased
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.data
AbstractStringExtractor This class implements the reader that extracts strings.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
ParameterSetParser.NotInstantiableException An `Exception` that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.data.alphabets
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.data.sequences
AbstractStringExtractor This class implements the reader that extracts strings.
SymbolExtractor This class enables you to extract elements (symbols) from a given `String` similar to a `StringTokenizer`.

Classes in de.jstacs.io used by de.jstacs.data.sequences.annotation
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.io
AbstractStringExtractor This class implements the reader that extracts strings.
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
ParameterSetParser.NotInstantiableException An `Exception` that is thrown if an instance of some class could not be created.
ParameterSetParser.WrongParameterTypeException An `Exception` that is thrown if the `DataType` of a `Parameter` is not appropriate for some purpose.

Classes in de.jstacs.io used by de.jstacs.motifDiscovery.history
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.parameters
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
ParameterSetParser.NotInstantiableException An `Exception` that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.parameters.validation
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

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

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

Classes in de.jstacs.io used by de.jstacs.sequenceScores.differentiable
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.differentiable.logistic
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
ParameterSetParser.NotInstantiableException An `Exception` that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.
ParameterSetParser.NotInstantiableException An `Exception` that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.phylo
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

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

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

Classes in de.jstacs.io used by de.jstacs.utils.galaxy
NonParsableException A `NonParsableException` is thrown if some object could not be restored (parsed) from a `StringBuffer`.

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