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Packages that use de.jstacs | |
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de.jstacs | This package is the root package for the most and important packages. |
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.scoringFunctionBased.logPrior | Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors |
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.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.utils | |
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.parameters.validation | Provides classes for the validation of Parameter values |
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. |
Classes in de.jstacs used by de.jstacs | |
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DataType
This enum defines a number of datatypes that can be used for Parameter and Result . |
Classes in de.jstacs used by de.jstacs.classifier | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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NotTrainedException
A NotTrainedException is thrown if the user tries to use an untrained model. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.classifier.assessment | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
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WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.classifier.modelBased | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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NotTrainedException
A NotTrainedException is thrown if the user tries to use an untrained model. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.cll | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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NotTrainedException
A NotTrainedException is thrown if the user tries to use an untrained model. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
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WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.classifier.scoringFunctionBased.logPrior | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.data | |
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InstantiableFromParameterSet
Interface for all classes that can be instantiated from a ParameterSet . |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
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WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.data.alphabets | |
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InstantiableFromParameterSet
Interface for all classes that can be instantiated from a ParameterSet . |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
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WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.data.bioJava | |
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WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.data.sequences | |
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WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.data.sequences.annotation | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.io | |
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InstantiableFromParameterSet
Interface for all classes that can be instantiated from a ParameterSet . |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.models | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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NotTrainedException
A NotTrainedException is thrown if the user tries to use an untrained model. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
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WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.models.discrete | |
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InstantiableFromParameterSet
Interface for all classes that can be instantiated from a ParameterSet . |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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NotTrainedException
A NotTrainedException is thrown if the user tries to use an untrained model. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
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WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous | |
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InstantiableFromParameterSet
Interface for all classes that can be instantiated from a ParameterSet . |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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NotTrainedException
A NotTrainedException is thrown if the user tries to use an untrained model. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
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WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous.parameters | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.models.discrete.inhomogeneous.shared | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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NotTrainedException
A NotTrainedException is thrown if the user tries to use an untrained model. |
|
Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
|
WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.models.mixture | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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NotTrainedException
A NotTrainedException is thrown if the user tries to use an untrained model. |
|
Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
|
WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.models.mixture.gibbssampling | |
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InstantiableFromParameterSet
Interface for all classes that can be instantiated from a ParameterSet . |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.models.utils | |
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NotTrainedException
A NotTrainedException is thrown if the user tries to use an untrained model. |
|
WrongAlphabetException
A WrongAlphabetException is thrown if a data file did not match the given alphabet. |
Classes in de.jstacs used by de.jstacs.parameters | |
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DataType
This enum defines a number of datatypes that can be used for Parameter and Result . |
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InstantiableFromParameterSet
Interface for all classes that can be instantiated from a ParameterSet . |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
|
Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.parameters.validation | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
|
Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.results | |
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DataType
This enum defines a number of datatypes that can be used for Parameter and Result . |
|
NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
|
Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.scoringFunctions | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.scoringFunctions.homogeneous | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
Classes in de.jstacs used by de.jstacs.scoringFunctions.mix | |
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NonParsableException
A NonParsable exception is thrown if some object could not be restored from a StringBuffer. |
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Storable
This is the root interface for all immutable objects that must be stored in e.g. a file or a database. |
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