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## Uses of Package
de.jstacs.data

Packages that use de.jstacs.data
de.jstacs.algorithms.alignment | Provides classes for alignments
de.jstacs.algorithms.alignment.cost | Provides classes for cost functions used in alignments
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.gendismix | Provides an implementation of a classifier that allows to train the parameters of a set of `NormalizableScoringFunction`s by a unified generative-discriminative learning principle
de.jstacs.classifier.scoringFunctionBased.sampling | Provides the classes for `AbstractScoreBasedClassifier`s that are based on `SamplingScoringFunction`s and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.classifier.utils | Provides some useful classes for working with classifiers
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.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 | The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.models.hmm.states.emissions |
de.jstacs.models.hmm.states.emissions.continuous |
de.jstacs.models.hmm.states.emissions.discrete |
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.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.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 `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.scoringFunctions.mix.motifSearch |

Classes in de.jstacs.data used by de.jstacs.algorithms.alignment
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.algorithms.alignment.cost
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier.assessment
Sample This is the class for any sample of `Sequence`s.
Sample.PartitionMethod This `enum` defines different partition methods for a `Sample`.

Classes in de.jstacs.data used by de.jstacs.classifier.modelBased
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier.scoringFunctionBased
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
AlphabetContainer.AlphabetContainerType This `enum` defines types of `AlphabetContainer`s.
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier.scoringFunctionBased.gendismix
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.classifier.scoringFunctionBased.sampling
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.classifier.utils
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.data
Alphabet Class for a set of symbols, i.e. an `Alphabet`.
Alphabet.AlphabetParameterSet The super class for the `InstanceParameterSet` of any `Alphabet`.
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
AlphabetContainer.AlphabetContainerType This `enum` defines types of `AlphabetContainer`s.
AlphabetContainerParameterSet Class for the `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` of an `AlphabetContainer`.
AlphabetContainerParameterSet.AlphabetArrayParameterSet Class for the parameters of an array of `Alphabet`s of defined length.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet Class for the parameter set of an array of `Alphabet`s where each `Alphabet` may be used for one or more sections of positions.
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.
EmptySampleException An `EmptySampleException` will be thrown if no `Sequence` is in a `Sample` (i.e. the `Sample` is empty).
RecyclableSequenceEnumerator This interface extends `Enumeration` of `Sequence`s by declaring an additional method that allows to reuse the Enumeration.
Sample This is the class for any sample of `Sequence`s.
Sample.PartitionMethod This `enum` defines different partition methods for a `Sample`.
Sample.WeightedSampleFactory.SortOperation This `enum` defines the different types of sort operations that can be performed while creating a `Sample.WeightedSampleFactory`.
Sequence This is the main class for all sequences.
Sequence.RecursiveSequence This is the main class for subsequences, composite sequences, ... .
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
Alphabet Class for a set of symbols, i.e. an `Alphabet`.
Alphabet.AlphabetParameterSet The super class for the `InstanceParameterSet` of any `Alphabet`.

Classes in de.jstacs.data used by de.jstacs.data.bioJava
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.data.sequences
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
EmptySampleException An `EmptySampleException` will be thrown if no `Sequence` is in a `Sample` (i.e. the `Sample` is empty).
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.
Sequence.RecursiveSequence This is the main class for subsequences, composite sequences, ... .
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 `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.io
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .

Classes in de.jstacs.data used by de.jstacs.models
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete.homogeneous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
EmptySampleException An `EmptySampleException` will be thrown if no `Sequence` is in a `Sample` (i.e. the `Sample` is empty).
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete.homogeneous.parameters
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .

Classes in de.jstacs.data used by de.jstacs.models.discrete.inhomogeneous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.discrete.inhomogeneous.parameters
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .

Classes in de.jstacs.data used by de.jstacs.models.discrete.inhomogeneous.shared
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.models.hmm
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.models.hmm.models
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.models.hmm.states
Sequence This is the main class for all sequences.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

Classes in de.jstacs.data used by de.jstacs.models.hmm.states.emissions
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.hmm.states.emissions.continuous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.hmm.states.emissions.discrete
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.hmm.transitions
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.hmm.transitions.elements
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.mixture
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.mixture.motif
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.models.utils
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.motifDiscovery
RecyclableSequenceEnumerator This interface extends `Enumeration` of `Sequence`s by declaring an additional method that allows to reuse the Enumeration.
Sample This is the class for any sample of `Sequence`s.
Sample.WeightedSampleFactory This class enables you to eliminate `Sequence`s that occur more than once in one or more `Sample`s.
Sample.WeightedSampleFactory.SortOperation This `enum` defines the different types of sort operations that can be performed while creating a `Sample.WeightedSampleFactory`.
Sequence This is the main class for all sequences.
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 `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
AlphabetContainer.AlphabetContainerType This `enum` defines types of `AlphabetContainer`s.

Classes in de.jstacs.data used by de.jstacs.results
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.sampling
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures
Sample This is the class for any sample of `Sequence`s.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.homogeneous
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.mix
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.mix.motifSearch
AlphabetContainer The container for `Alphabet`s used in a `Sequence`, `Sample`, `AbstractModel` or ... .
Sample This is the class for any sample of `Sequence`s.
Sequence This is the main class for all sequences.
WrongLengthException A `WrongLengthException` is thrown if a given (sub)sequence length is not correct.

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