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 Classifiers that are based on Models
de.jstacs.classifier.scoringFunctionBased	Provides the classes for Classifiers that are based on ScoringFunctions.
de.jstacs.classifier.scoringFunctionBased.gendismix	Provides an implementation of a classifier that allows to train the parameters of a set of NormalizableScoringFunctions by a unified generative-discriminative learning principle
de.jstacs.classifier.scoringFunctionBased.sampling	Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingScoringFunctions 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 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.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 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

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 Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

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 Sequences.

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 Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

Sequence
This is the main class for all sequences.

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

AlphabetContainer
The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .

AlphabetContainer.AlphabetContainerType
This enum defines types of AlphabetContainers.

Sample
This is the class for any sample of Sequences.

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 Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

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

AlphabetContainer
The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

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 Sequences.

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 Alphabets used in a Sequence, Sample, AbstractModel or ... .

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.

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 Sequences by declaring an additional method that allows to reuse the Enumeration.

Sample
This is the class for any sample of Sequences.

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 Sequences.

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

AlphabetContainer
The container for Alphabets 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 Sequences.

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 Alphabets 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 Alphabets used in a Sequence, Sample, AbstractModel or ... .

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

AlphabetContainer
The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

Sequence
This is the main class for all sequences.

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

AlphabetContainer
The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

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 Alphabets 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 Sequences.

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 Alphabets used in a Sequence, Sample, AbstractModel or ... .

Classes in de.jstacs.data used by de.jstacs.models.discrete.inhomogeneous

AlphabetContainer
The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

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 Alphabets 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 Sequences.

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

AlphabetContainer
The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

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 Sequences.

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 Alphabets 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 Alphabets 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 Alphabets 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 Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

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 Sequences.

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 Sequences.

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 Sequences by declaring an additional method that allows to reuse the Enumeration.

Sample
This is the class for any sample of Sequences.

Sample.WeightedSampleFactory
This class enables you to eliminate Sequences that occur more than once in one or more Samples.

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 Alphabets used in a Sequence, Sample, AbstractModel or ... .

AlphabetContainer.AlphabetContainerType
This enum defines types of AlphabetContainers.

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

Sample
This is the class for any sample of Sequences.

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

Sample
This is the class for any sample of Sequences.

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

AlphabetContainer
The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

Sequence
This is the main class for all sequences.

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

AlphabetContainer
The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

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 Sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Sample
This is the class for any sample of Sequences.

Classes in de.jstacs.data used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures

Sample
This is the class for any sample of Sequences.

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

AlphabetContainer
The container for Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

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 Sequences.

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 Alphabets used in a Sequence, Sample, AbstractModel or ... .

Sample
This is the class for any sample of Sequences.

Sequence
This is the main class for all sequences.

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