Uses of Package
de.jstacs.io

Packages that use de.jstacs.io

Package	Description
de.jstacs	This package is the root package for the most and important packages.
de.jstacs.algorithms.alignment	Provides classes for alignments.
de.jstacs.algorithms.alignment.cost	Provides classes for cost functions used in alignments.
de.jstacs.algorithms.optimization.termination	Provides classes for termination conditions that can be used in algorithms.
de.jstacs.classifiers	This package provides the framework for any classifier.
de.jstacs.classifiers.assessment	This package allows to assess classifiers. It contains the class ClassifierAssessment that is used as a super-class of all implemented methodologies of an assessment to assess classifiers.
de.jstacs.classifiers.differentiableSequenceScoreBased	Provides the classes for Classifiers that are based on SequenceScores. It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior.
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix	Provides an implementation of a classifier that allows to train the parameters of a set of DifferentiableStatisticalModels by a unified generative-discriminative learning principle.
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior	Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors.
de.jstacs.classifiers.differentiableSequenceScoreBased.msp	Provides an implementation of a classifier that allows to train the parameters of a set of DifferentiableStatisticalModels either by maximum supervised posterior (MSP) or by maximum conditional likelihood (MCL).
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling	Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingDifferentiableStatisticalModels and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.classifiers.performanceMeasures	This package provides the implementations of performance measures that can be used to assess any classifier.
de.jstacs.classifiers.trainSMBased	Provides the classes for Classifiers that are based on TrainableStatisticalModels.
de.jstacs.clustering.hierachical
de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
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.sequences	Provides classes for representing sequences. The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well. As sub-package provides the facilities to annotate 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.motifDiscovery.history
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.sampling	This package contains many classes that can be used while a sampling.
de.jstacs.sequenceScores.differentiable
de.jstacs.sequenceScores.differentiable.logistic
de.jstacs.sequenceScores.statisticalModels.differentiable	Provides all DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels	Provides DifferentiableStatisticalModels that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures	Provides the facilities to learn the structure of a BayesianNetworkDiffSM.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures	Provides the facilities to learn the structure of a BayesianNetworkDiffSM as a Bayesian tree using a number of measures to define a rating of structures.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures	Provides the facilities to learn the structure of a BayesianNetworkDiffSM as a permuted Markov model using a number of measures to define a rating of structures.
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous	Provides DifferentiableStatisticalModels that are homogeneous, i.e.
de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif
de.jstacs.sequenceScores.statisticalModels.trainable	Provides all TrainableStatisticalModels, which can be learned from a single DataSet.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous	This package contains various inhomogeneous models.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared
de.jstacs.sequenceScores.statisticalModels.trainable.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models	The package provides different implementations of hidden Markov models based on AbstractHMM.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training	The package provides all classes used to determine the training algorithm of a hidden Markov model.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions	The package provides all interfaces and classes for transitions used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements
de.jstacs.sequenceScores.statisticalModels.trainable.mixture	This package is the super package for any mixture model.
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior
de.jstacs.sequenceScores.statisticalModels.trainable.phylo
de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser
de.jstacs.tools
de.jstacs.tools.ui.galaxy
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

Classes in de.jstacs.io used by de.jstacs

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.algorithms.alignment

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.algorithms.alignment.cost

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.algorithms.optimization.termination

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.classifiers

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.classifiers.assessment

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
ParameterSetParser.NotInstantiableException An Exception that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased.msp

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.classifiers.differentiableSequenceScoreBased.sampling

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.classifiers.performanceMeasures

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.classifiers.trainSMBased

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.clustering.hierachical

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

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

Class and Description
AbstractStringExtractor This class implements the reader that extracts strings.
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
ParameterSetParser.NotInstantiableException An Exception that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.data.alphabets

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

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

Class and Description
AbstractStringExtractor This class implements the reader that extracts strings.
SymbolExtractor This class enables you to extract elements (symbols) from a given String similar to a StringTokenizer.

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

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.io

Class and Description
AbstractStringExtractor This class implements the reader that extracts strings.
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
ParameterSetParser.NotInstantiableException An Exception that is thrown if an instance of some class could not be created.
ParameterSetParser.WrongParameterTypeException An Exception that is thrown if the DataType of a Parameter is not appropriate for some purpose.
RegExFilenameFilter.Directory A switch to decide whether the results of a RegExFilenameFilter are forbidden, allowed or required to be a directory.

Classes in de.jstacs.io used by de.jstacs.motifDiscovery.history

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.parameters

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
ParameterSetParser.NotInstantiableException An Exception that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.parameters.validation

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

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

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

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

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.differentiable

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.differentiable.logistic

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
ParameterSetParser.NotInstantiableException An Exception that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.
ParameterSetParser.NotInstantiableException An Exception that is thrown if an instance of some class could not be created.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.phylo

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.tools

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.tools.ui.galaxy

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.

Classes in de.jstacs.io used by de.jstacs.utils

Class and Description
NonParsableException A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.