Uses of Package
de.jstacs.io

Packages that use de.jstacs.io
de.jstacs This package is the root package for the most and important packages. 
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. 
de.jstacs.classifiers.differentiableSequenceScoreBased Provides the classes for Classifiers that are based on SequenceScores. 
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 TrainableStatisticalModel
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.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.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. model probabilities or scores independent of the position within a sequence 
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.utils This package contains a bundle of useful classes and interfaces like ... 
de.jstacs.utils.galaxy   
 

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

Classes in de.jstacs.io used by de.jstacs.motifDiscovery.history
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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.galaxy
NonParsableException
          A NonParsableException is thrown if some object could not be restored (parsed) from a StringBuffer.