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Packages that use de.jstacs.data | |
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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 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.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 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.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 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 | |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data used by de.jstacs.classifier | |
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AlphabetContainer
The container for Alphabet s used in a Sequence ,
Sample , AbstractModel or ... . |
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Sample
This is the class for any sample of Sequence s. |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data used by de.jstacs.classifier.assessment | |
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Sample
This is the class for any sample of Sequence s. |
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Sample.PartitionMethod
This enum defines different partition methods for a
Sample . |
Classes in de.jstacs.data used by de.jstacs.classifier.modelBased | |
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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 | |
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AlphabetContainer
The container for Alphabet s used in a Sequence ,
Sample , AbstractModel or ... . |
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AlphabetContainer.AlphabetContainerType
This enum defines types of AlphabetContainer s. |
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Sample
This is the class for any sample of Sequence s. |
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Sequence
This is the main class for all sequences. |
Classes in de.jstacs.data used by de.jstacs.classifier.scoringFunctionBased.cll | |
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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.utils | |
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Sample
This is the class for any sample of Sequence s. |
Classes in de.jstacs.data used by de.jstacs.data | |
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Alphabet
Class for a set of symbols, i.e. an Alphabet . |
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Alphabet.AlphabetParameterSet
The super class for the InstanceParameterSet of any
Alphabet . |
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AlphabetContainer
The container for Alphabet s used in a Sequence ,
Sample , AbstractModel or ... . |
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AlphabetContainer.AlphabetContainerType
This enum defines types of AlphabetContainer s. |
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AlphabetContainerParameterSet
Class for the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet of an AlphabetContainer . |
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AlphabetContainerParameterSet.AlphabetArrayParameterSet
Class for the parameters of an array of Alphabet s of defined
length. |
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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. |
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EmptySampleException
An EmptySampleException will be thrown if no Sequence is in a
Sample (i.e. the Sample is empty). |
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Sample
This is the class for any sample of Sequence s. |
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Sample.PartitionMethod
This enum defines different partition methods for a
Sample . |
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Sample.WeightedSampleFactory.SortOperation
This enum defines the different types of sort operations
that can be performed while creating a Sample.WeightedSampleFactory . |
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Sequence
This is the main class for all sequences. |
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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 | |
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Alphabet
Class for a set of symbols, i.e. an Alphabet . |
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Alphabet.AlphabetParameterSet
The super class for the InstanceParameterSet of any
Alphabet . |
Classes in de.jstacs.data used by de.jstacs.data.bioJava | |
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Sample
This is the class for any sample of Sequence s. |
Classes in de.jstacs.data used by de.jstacs.data.sequences | |
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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 | |
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AlphabetContainer
The container for Alphabet s used in a Sequence ,
Sample , AbstractModel or ... . |
Classes in de.jstacs.data used by de.jstacs.models | |
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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 | |
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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 | |
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EmptySampleException
An EmptySampleException will be thrown if no Sequence is in a
Sample (i.e. the Sample is empty). |
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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 | |
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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 | |
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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 | |
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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 | |
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Sample
This is the class for any sample of Sequence s. |
Classes in de.jstacs.data used by de.jstacs.models.mixture | |
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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.gibbssampling | |
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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.models.mixture.motif | |
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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 | |
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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 | |
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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.parameters | |
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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 | |
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Sample
This is the class for any sample of Sequence s. |
Classes in de.jstacs.data used by de.jstacs.scoringFunctions | |
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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 | |
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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 | |
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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 | |
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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 | |
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Sample
This is the class for any sample of Sequence s. |
Classes in de.jstacs.data used by de.jstacs.scoringFunctions.homogeneous | |
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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 | |
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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 | |
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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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