Uses of Package
de.jstacs.data

Packages that use de.jstacs.data
de.jstacs.algorithms Provides classes for algorithms on graphs. 
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 Model
de.jstacs.classifier.scoringFunctionBased Provides the classes for Classifiers that are based on ScoringFunctions. 
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.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.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.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.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.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
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.cll
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.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.
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.
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.
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 ... .
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
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.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.gibbssampling
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.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
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.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.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.