Uses of Package
de.jstacs.data

Packages that use de.jstacs.data

de.jstacs.classifiers	This package provides the framework for any classifier.
de.jstacs.classifiers.assessment	This package allows to assess classifiers. It contains the class ClassifierAssessment that is used as a super-class of all implemented methodologies of an assessment to assess classifiers.
de.jstacs.classifiers.differentiableSequenceScoreBased	Provides the classes for Classifiers that are based on SequenceScores. It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior.
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix	Provides an implementation of a classifier that allows to train the parameters of a set of DifferentiableStatisticalModels by a unified generative-discriminative learning principle.
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling	Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingDifferentiableStatisticalModels and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.classifiers.trainSMBased	Provides the classes for Classifiers that are based on TrainableStatisticalModels.
de.jstacs.classifiers.utils	Provides some useful classes for working with classifiers.
de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
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. The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well. As sub-package provides the facilities to annotate 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.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.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	Provides all SequenceScores, which can be used to score a Sequence, typically using some model assumptions.
de.jstacs.sequenceScores.differentiable
de.jstacs.sequenceScores.differentiable.logistic
de.jstacs.sequenceScores.statisticalModels	Provides all StatisticalModels, which can compute a proper (i.e., normalized) likelihood over the input space of sequences. StatisticalModels can be further differentiated into TrainableStatisticalModels, which can be learned from a single input DataSet, and DifferentiableStatisticalModels, which define a proper likelihood but can also compute gradients like DifferentiableSequenceScores.
de.jstacs.sequenceScores.statisticalModels.differentiable	Provides all DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels	Provides DifferentiableStatisticalModels 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 DifferentiableStatisticalModels that are homogeneous, i.e.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif
de.jstacs.sequenceScores.statisticalModels.trainable	Provides all TrainableStatisticalModels, 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	The package provides all interfaces and classes for states used in hidden Markov models.
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.mixture	This package is the super package for any mixture model.
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

Classes in de.jstacs.data used by de.jstacs.classifiers

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.classifiers.assessment

DataSet
This is the class for any data set of Sequences.

DataSet.PartitionMethod
This enum defines different partition methods for a DataSet.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.classifiers.differentiableSequenceScoreBased

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

AlphabetContainer.AlphabetContainerType
This enum defines types of AlphabetContainers.

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.classifiers.differentiableSequenceScoreBased.sampling

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.classifiers.trainSMBased

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.classifiers.utils

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.data

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

AlphabetContainer.AbstractAlphabetContainerParameterSet
This class is the super class of any InstanceParameterSet for AlphabetContainer.

AlphabetContainer.AlphabetContainerType
This enum defines types of AlphabetContainers.

AlphabetContainerParameterSet
Class for the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet of an AlphabetContainer.

AlphabetContainerParameterSet.AlphabetArrayParameterSet
Class for the parameters of an array of Alphabets of defined length.

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
Class for the parameter set of an array of Alphabets where each Alphabet may be used for one or more sections of positions.

DataSet
This is the class for any data set of Sequences.

DataSet.PartitionMethod
This enum defines different partition methods for a DataSet.

DataSet.WeightedDataSetFactory.SortOperation
This enum defines the different types of sort operations that can be performed while creating a DataSet.WeightedDataSetFactory.

DinucleotideProperty
This enum defines physicochemical, conformational, and letter-based dinucleotide properties of nucleotide sequences.

DinucleotideProperty.HowCreated
This enum defines the origins of nucleotide properties

DinucleotideProperty.Smoothing
Abstract class for methods that smooth a series of real values.

DinucleotideProperty.Type
This enum defines the types of dinucleotide properties.

EmptyDataSetException
An EmptyDataSetException will be thrown if no Sequence is in a DataSet (i.e.

RecyclableSequenceEnumerator
This interface extends Enumeration of Sequences by declaring an additional method that allows to reuse the Enumeration.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

WrongLengthException
A WrongLengthException is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.data.alphabets

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

AlphabetContainer.AbstractAlphabetContainerParameterSet
This class is the super class of any InstanceParameterSet for AlphabetContainer.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.data.bioJava

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.data.sequences

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

EmptyDataSetException
An EmptyDataSetException will be thrown if no Sequence is in a DataSet (i.e.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

WrongLengthException
A WrongLengthException is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.data.sequences.annotation

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

Classes in de.jstacs.data used by de.jstacs.io

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

Classes in de.jstacs.data used by de.jstacs.motifDiscovery

DataSet
This is the class for any data set of Sequences.

DataSet.WeightedDataSetFactory
This class enables you to eliminate Sequences that occur more than once in one or more DataSets.

DataSet.WeightedDataSetFactory.SortOperation
This enum defines the different types of sort operations that can be performed while creating a DataSet.WeightedDataSetFactory.

RecyclableSequenceEnumerator
This interface extends Enumeration of Sequences by declaring an additional method that allows to reuse the Enumeration.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

WrongLengthException
A WrongLengthException is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.parameters

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

AlphabetContainer.AlphabetContainerType
This enum defines types of AlphabetContainers.

Classes in de.jstacs.data used by de.jstacs.results

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sampling

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sequenceScores

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.differentiable

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

WrongLengthException
A WrongLengthException is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.differentiable.logistic

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

WrongLengthException
A WrongLengthException is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

EmptyDataSetException
An EmptyDataSetException will be thrown if no Sequence is in a DataSet (i.e.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

WrongLengthException
A WrongLengthException is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states

WrongLengthException
A WrongLengthException is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif

DataSet
This is the class for any data set of Sequences.

WrongAlphabetException
A WrongAlphabetException is thrown if the given Alphabet or AlphabetContainer does not support some data.

Classes in de.jstacs.data used by de.jstacs.utils

AlphabetContainer
The container for Alphabets used in a Sequence, DataSet, AbstractTrainableStatisticalModel or ...

DataSet
This is the class for any data set of Sequences.