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## Uses of Class
de.jstacs.NonParsableException

Packages that use NonParsableException
de.jstacs.algorithms.optimization.termination |
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.gendismix | Provides an implementation of a classifier that allows to train the parameters of a set of `NormalizableScoringFunction`s by a unified generative-discriminative learning principle
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.classifier.scoringFunctionBased.msp | Provides an implementation of a classifier that allows to train the parameters of a set of `ScoringFunctions` either by maximum supervised posterior (MSP) or by maximum conditional likelihood (MCL)
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.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.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.mixture.motif.positionprior |
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.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 |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ...

Uses of NonParsableException in de.jstacs.algorithms.optimization.termination

Constructors in de.jstacs.algorithms.optimization.termination that throw NonParsableException
`AbsoluteValueCondition.AbsoluteValueConditionParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`AbsoluteValueCondition(StringBuffer xml)` Deprecated. The standard constructor for the interface `Storable`.
`AbstractTerminationCondition.AbstractTerminationConditionParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`AbstractTerminationCondition(StringBuffer xml)` The standard constructor for the interface `Storable`.
`CombinedCondition.CombinedConditionParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`CombinedCondition(StringBuffer xml)` The standard constructor for the interface `Storable`.
`IterationCondition.IterationConditionParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`IterationCondition(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SmallDifferenceOfFunctionEvaluationsCondition.SmallDifferenceOfFunctionEvaluationsConditionParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SmallDifferenceOfFunctionEvaluationsCondition(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SmallGradientConditon.SmallGradientConditonParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SmallGradientConditon(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SmallStepCondition.SmallStepConditionParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SmallStepCondition(StringBuffer xml)` The standard constructor for the interface `Storable`.
`TimeCondition.TimeConditionParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`TimeCondition(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.classifier

Methods in de.jstacs.classifier that throw NonParsableException
`protected void` | `MappingClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)`
`protected void` | `AbstractScoreBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)`
`protected abstract void` | `AbstractClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)` Extracts further information of a classifier from an XML representation.
`protected void` | `AbstractScoreBasedClassifier.DoubleTableResult.fromXML(StringBuffer representation)`

Constructors in de.jstacs.classifier that throw NonParsableException
`AbstractClassifier(StringBuffer xml)` The standard constructor for the interface `Storable`.
`AbstractScoreBasedClassifier.DoubleTableResult(StringBuffer representation)` The standard constructor for the interface `Storable` .
`AbstractScoreBasedClassifier(StringBuffer xml)` The standard constructor for the interface `Storable`.
`ConfusionMatrix(StringBuffer representation)` The standard constructor for the interface `Storable`.
`MappingClassifier(StringBuffer representation)` The standard constructor for the interface `Storable`.
`MeasureParameters(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.classifier.assessment

Constructors in de.jstacs.classifier.assessment that throw NonParsableException
`ClassifierAssessmentAssessParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`KFoldCVAssessParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`RepeatedHoldOutAssessParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`RepeatedSubSamplingAssessParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`Sampled_RepeatedHoldOutAssessParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.classifier.modelBased

Methods in de.jstacs.classifier.modelBased that throw NonParsableException
`protected void` | `ModelBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)`

Constructors in de.jstacs.classifier.modelBased that throw NonParsableException
`ModelBasedClassifier(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.classifier.scoringFunctionBased

Methods in de.jstacs.classifier.scoringFunctionBased that throw NonParsableException
`protected void` | `ScoreClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)`

Constructors in de.jstacs.classifier.scoringFunctionBased that throw NonParsableException
`ScoreClassifier(StringBuffer xml)` The standard constructor for the interface `Storable`.
`ScoreClassifierParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.classifier.scoringFunctionBased.gendismix

Methods in de.jstacs.classifier.scoringFunctionBased.gendismix that throw NonParsableException
`protected void` | `GenDisMixClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)`

Constructors in de.jstacs.classifier.scoringFunctionBased.gendismix that throw NonParsableException
`GenDisMixClassifier(StringBuffer xml)` This is the constructor for `Storable`.
`GenDisMixClassifierParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.classifier.scoringFunctionBased.logPrior

Constructors in de.jstacs.classifier.scoringFunctionBased.logPrior that throw NonParsableException
`SeparateGaussianLogPrior(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SeparateLaplaceLogPrior(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SeparateLogPrior(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SimpleGaussianSumLogPrior(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.classifier.scoringFunctionBased.msp

Constructors in de.jstacs.classifier.scoringFunctionBased.msp that throw NonParsableException
`MSPClassifier(StringBuffer xml)` This is the constructor for `Storable`.

Uses of NonParsableException in de.jstacs.data

Methods in de.jstacs.data that throw NonParsableException
`protected void` | `AlphabetContainerParameterSet.fromXML(StringBuffer representation)`
`void` | `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet.fromXML(StringBuffer representation)`
`void` | `AlphabetContainerParameterSet.AlphabetArrayParameterSet.fromXML(StringBuffer representation)`

Constructors in de.jstacs.data that throw NonParsableException
`Alphabet.AlphabetParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .
`AlphabetContainer(StringBuffer xml)` The standard constructor for the interface `Storable`.
`AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .
`AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .
`AlphabetContainerParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.data.alphabets

Constructors in de.jstacs.data.alphabets that throw NonParsableException
`ComplementableDiscreteAlphabet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`ContinuousAlphabet.ContinuousAlphabetParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .
`ContinuousAlphabet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`DiscreteAlphabet.DiscreteAlphabetParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .
`DiscreteAlphabet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`DiscreteAlphabetMapping(StringBuffer xml)` The standard constructor for the interface `Storable`.
`DNAAlphabet.DNAAlphabetParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .
`DNAAlphabet(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.data.sequences.annotation

Methods in de.jstacs.data.sequences.annotation that throw NonParsableException
`protected void` | `StrandedLocatedSequenceAnnotationWithLength.fromXML(StringBuffer representation)`
`protected void` | `SequenceAnnotation.fromXML(StringBuffer source)`
`protected void` | `LocatedSequenceAnnotationWithLength.fromXML(StringBuffer representation)`
`protected void` | `LocatedSequenceAnnotation.fromXML(StringBuffer representation)`

Constructors in de.jstacs.data.sequences.annotation that throw NonParsableException
`CisRegulatoryModuleAnnotation(StringBuffer representation)` The standard constructor for the interface `Storable`.
`IntronAnnotation(StringBuffer representation)` The standard constructor for the interface `Storable`.
`LocatedSequenceAnnotation(StringBuffer representation)` The standard constructor for the interface `Storable`.
`LocatedSequenceAnnotationWithLength(StringBuffer representation)` The standard constructor for the interface `Storable`.
`MotifAnnotation(StringBuffer representation)` The standard constructor for the interface `Storable`.
`ReferenceSequenceAnnotation(StringBuffer representation)` The standard constructor for the interface `Storable`.
`SequenceAnnotation(StringBuffer representation)` The standard constructor for the interface `Storable`.
`SinglePositionSequenceAnnotation(StringBuffer representation)` The standard constructor for the interface `Storable`.
`StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.io

Methods in de.jstacs.io that throw NonParsableException
`static StringBuffer` | `XMLParser.extractForTag(StringBuffer source, String tag)` Extracts the contents of `source` between `tag` start and end tags.
`static StringBuffer` | `XMLParser.extractForTag(StringBuffer source, String tag, Map<String,String> attributes, Map<String,String> filterAttributes)` Extracts the contents of `source` between `tag` start and end tags.
`static Object` | `XMLParser.extractObjectAndAttributesForTags(StringBuffer xml, String tag, Map<String,String> attributes, Map<String,String> filterAttributes)` Returns the parsed value between the tags.
`static
`<T> T`
` | `XMLParser.extractObjectAndAttributesForTags(StringBuffer xml, String tag, Map<String,String> attributes, Map<String,String> filterAttributes, Class<T> k)` Returns the parsed value between the tags.
`static
`<T,S> T`
` | `XMLParser.extractObjectAndAttributesForTags(StringBuffer xml, String tag, Map<String,String> attributes, Map<String,String> filterAttributes, Class<T> k, Class<S> outerClass, S outerInstance)` Returns the parsed value between the tags as an inner instance of the object `outerInstance`.
`static Object` | `XMLParser.extractObjectForTags(StringBuffer xml, String tag)` Returns the parsed value between the tags.
`static
`<T> T`
` | `XMLParser.extractObjectForTags(StringBuffer xml, String tag, Class<T> k)` Returns the parsed value between the tags.
`static boolean` | `XMLParser.hasTag(StringBuffer source, String tag, Map<String,String> attributes, Map<String,String> filterAttributes)` This method allows to check whether an XML contains a tagged entry.

Uses of NonParsableException in de.jstacs.models

Methods in de.jstacs.models that throw NonParsableException
`protected void` | `VariableLengthWrapperModel.fromXML(StringBuffer xml)`
`void` | `UniformModel.fromXML(StringBuffer representation)`
`protected void` | `NormalizableScoringFunctionModel.fromXML(StringBuffer xml)`
`void` | `CompositeModel.fromXML(StringBuffer representation)`
`protected abstract void` | `AbstractModel.fromXML(StringBuffer xml)` This method should only be used by the constructor that works on a `StringBuffer`.

Constructors in de.jstacs.models that throw NonParsableException
`AbstractModel(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.
`CompositeModel(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.
`NormalizableScoringFunctionModel(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.
`UniformModel(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.
`VariableLengthWrapperModel(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.models.discrete

Methods in de.jstacs.models.discrete that throw NonParsableException
`protected abstract void` | `Constraint.extractAdditionalInfo(StringBuffer xml)` This method parses additional information from the `StringBuffer` that is not parsed in the base class.
`protected void` | `DiscreteGraphicalModel.fromXML(StringBuffer representation)`
`protected void` | `DiscreteGraphicalModel.set(DGMParameterSet params, boolean trained)` Sets the parameters as internal parameters and does some essential computations.
`protected abstract void` | `DiscreteGraphicalModel.setFurtherModelInfos(StringBuffer xml)` This method replaces the internal model information with those from a `StringBuffer`.

Constructors in de.jstacs.models.discrete that throw NonParsableException
`Constraint(StringBuffer xml)` The standard constructor for the interface `Storable`.
`DGMParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.
`DiscreteGraphicalModel(DGMParameterSet params)` The default constructor.
`DiscreteGraphicalModel(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.models.discrete.homogeneous

Methods in de.jstacs.models.discrete.homogeneous that throw NonParsableException
`protected void` | `HomogeneousModel.HomCondProb.extractAdditionalInfo(StringBuffer xml)`
`protected void` | `HomogeneousModel.set(DGMParameterSet params, boolean trained)`
`protected void` | `HomogeneousMM.set(DGMParameterSet params, boolean trained)`
`protected void` | `HomogeneousMM.setFurtherModelInfos(StringBuffer xml)`

Constructors in de.jstacs.models.discrete.homogeneous that throw NonParsableException
`HomogeneousMM(HomMMParameterSet params)` Creates a new homogeneous Markov model from a parameter set.
`HomogeneousMM(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.
`HomogeneousModel.HomCondProb(StringBuffer xml)` The standard constructor for the interface `Storable` .
`HomogeneousModel(HomogeneousModelParameterSet params)` Creates a homogeneous model from a parameter set.
`HomogeneousModel(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.models.discrete.homogeneous.parameters

Constructors in de.jstacs.models.discrete.homogeneous.parameters that throw NonParsableException
`HomMMParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.
`HomogeneousModelParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.models.discrete.inhomogeneous

Methods in de.jstacs.models.discrete.inhomogeneous that throw NonParsableException
`protected void` | `MEMConstraint.extractAdditionalInfo(StringBuffer xml)`
`protected void` | `InhConstraint.extractAdditionalInfo(StringBuffer xml)`
`protected void` | `InhCondProb.extractAdditionalInfo(StringBuffer xml)`
`protected void` | `InhomogeneousDGM.set(DGMParameterSet parameter, boolean trained)`
`protected void` | `FSDAGModel.set(DGMParameterSet params, boolean trained)`
`protected void` | `BayesianNetworkModel.set(DGMParameterSet parameter, boolean trained)`
`protected void` | `DAGModel.setFurtherModelInfos(StringBuffer xml)`

Constructors in de.jstacs.models.discrete.inhomogeneous that throw NonParsableException
`BayesianNetworkModel(BayesianNetworkModelParameterSet params)` Creates a new `BayesianNetworkModel` from a given `BayesianNetworkModelParameterSet`.
`BayesianNetworkModel(StringBuffer representation)` The standard constructor for the interface `Storable`.
`DAGModel(IDGMParameterSet params)` This is the main constructor.
`DAGModel(StringBuffer xml)` The standard constructor for the interface `Storable`.
`FSDAGModel(FSDAGMParameterSet params)` This is the main constructor.
`FSDAGModel(StringBuffer xml)` The standard constructor for the interface `Storable`.
`InhCondProb(StringBuffer xml)` The standard constructor for the interface `Storable`.
`InhConstraint(StringBuffer xml)` The standard constructor for the interface `Storable`.
`InhomogeneousDGM(IDGMParameterSet params)` Creates a new `InhomogeneousDGM` from a given `IDGMParameterSet`.
`InhomogeneousDGM(StringBuffer representation)` The standard constructor for the interface `Storable`.
`MEMConstraint(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.models.discrete.inhomogeneous.parameters

Constructors in de.jstacs.models.discrete.inhomogeneous.parameters that throw NonParsableException
`BayesianNetworkModelParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.
`FSDAGMParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.
`IDGMParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.models.discrete.inhomogeneous.shared

Methods in de.jstacs.models.discrete.inhomogeneous.shared that throw NonParsableException
`protected void` | `SharedStructureClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)`
`protected void` | `SharedStructureMixture.fromXML(StringBuffer representation)`

Constructors in de.jstacs.models.discrete.inhomogeneous.shared that throw NonParsableException
`SharedStructureClassifier(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SharedStructureMixture(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.models.mixture

Methods in de.jstacs.models.mixture that throw NonParsableException
`protected void` | `AbstractMixtureModel.extractFurtherInformation(StringBuffer xml)` This method is used in the subclasses to extract further information from the XML representation and to set these as values of the instance.
`protected void` | `AbstractMixtureModel.fromXML(StringBuffer representation)`

Constructors in de.jstacs.models.mixture that throw NonParsableException
`AbstractMixtureModel(StringBuffer xml)` The standard constructor for the interface `Storable`.
`MixtureModel(StringBuffer xml)` The constructor for the interface `Storable`.
`StrandModel(StringBuffer stringBuff)` The constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.models.mixture.gibbssampling

Methods in de.jstacs.models.mixture.gibbssampling that throw NonParsableException
`protected void` | `VarianceRatioBurnInTest.setFurtherInformation(StringBuffer xml)`
`protected abstract void` | `AbstractBurnInTest.setFurtherInformation(StringBuffer xml)` This method sets further information for the `AbstractBurnInTest`.
`protected void` | `FSDAGModelForGibbsSampling.setFurtherModelInfos(StringBuffer xml)`

Constructors in de.jstacs.models.mixture.gibbssampling that throw NonParsableException
`AbstractBurnInTest(StringBuffer rep)` This is the constructor for the `Storable` interface.
`AbstractBurnInTestParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`FSDAGModelForGibbsSampling(FSDAGModelForGibbsSamplingParameterSet params)` The default constructor.
`FSDAGModelForGibbsSampling(StringBuffer representation)` This is the constructor for the `Storable` interface.
`FSDAGModelForGibbsSamplingParameterSet(StringBuffer s)` The constructor for the `Storable` interface.
`SimpleBurnInTest(StringBuffer xml)` Deprecated. The standard constructor for the interface `Storable`.
`VarianceRatioBurnInTest(StringBuffer rep)` The standard constructor for the `Storable` interface.

Uses of NonParsableException in de.jstacs.models.mixture.motif

Methods in de.jstacs.models.mixture.motif that throw NonParsableException
`protected void` | `HiddenMotifMixture.extractFurtherInformation(StringBuffer xml)`

Constructors in de.jstacs.models.mixture.motif that throw NonParsableException
`HiddenMotifMixture(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SingleHiddenMotifMixture(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.models.mixture.motif.positionprior

Methods in de.jstacs.models.mixture.motif.positionprior that throw NonParsableException
`protected abstract void` | `PositionPrior.extractAdditionalInformation(StringBuffer xml)` This method extracts additional information from a `StringBuffer`.
`protected void` | `GaussianLikePositionPrior.extractAdditionalInformation(StringBuffer xml)`

Constructors in de.jstacs.models.mixture.motif.positionprior that throw NonParsableException
`GaussianLikePositionPrior(StringBuffer rep)` The standard constructor for the interface `Storable`.
`PositionPrior(StringBuffer rep)` The standard constructor for the interface `Storable`.
`UniformPositionPrior(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.motifDiscovery.history

Constructors in de.jstacs.motifDiscovery.history that throw NonParsableException
`CappedHistory(StringBuffer xml)` This is the constructor for the interface `Storable`.
`NoRevertHistory(StringBuffer xml)` This is the constructor for the interface `Storable`.
`RestrictedRepeatHistory(StringBuffer xml)` This is the constructor for the interface `Storable`.
`SimpleHistory(StringBuffer xml)` This is the constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.parameters

Methods in de.jstacs.parameters that throw NonParsableException
`protected void` | `EnumParameter.extractCollection(StringBuffer buf)`
`protected void` | `CollectionParameter.extractCollection(StringBuffer buf)` Extracts the internal `ParameterSet` from its XML representation ( `ParameterSet.toXML()`).
`protected void` | `SimpleParameter.fromXML(StringBuffer representation)`
`protected void` | `SequenceScoringParameterSet.fromXML(StringBuffer representation)`
`protected void` | `RangeParameter.fromXML(StringBuffer representation)`
`protected void` | `ParameterSetContainer.fromXML(StringBuffer representation)`
`protected void` | `ParameterSet.fromXML(StringBuffer representation)` Parses the instance fields of a `ParameterSet` from the XML representation as returned by `ParameterSet.toXML()`.
`protected void` | `Parameter.fromXML(StringBuffer source)` Parses a `Parameter` from a XML representation as returned by `Parameter.toXML()`.
`protected void` | `MultiSelectionCollectionParameter.fromXML(StringBuffer representation)`
`protected void` | `InstanceParameterSet.fromXML(StringBuffer representation)`
`protected void` | `FileParameter.fromXML(StringBuffer representation)`
`protected void` | `ExpandableParameterSet.fromXML(StringBuffer representation)`
`protected void` | `CollectionParameter.fromXML(StringBuffer representation)`
`protected void` | `ArrayParameterSet.fromXML(StringBuffer representation)`

Constructors in de.jstacs.parameters that throw NonParsableException
`ArrayParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`CollectionParameter(StringBuffer representation)` The standard constructor for the interface `Storable`.
`EnumParameter(StringBuffer representation)` The standard constructor for the interface `Storable`.
`ExpandableParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`FileParameter.FileRepresentation(StringBuffer buf)` The standard constructor for the interface `Storable` .
`FileParameter(StringBuffer buf)` The standard constructor for the interface `Storable`.
`InstanceParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`MultiSelectionCollectionParameter(StringBuffer representation)` The standard constructor for the interface `Storable`.
`ParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`ParameterSetContainer(StringBuffer representation)` The standard constructor for the interface `Storable`.
`RangeParameter(StringBuffer representation)` The standard constructor for the interface `Storable`.
`SequenceScoringParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`SimpleParameter(StringBuffer representation)` The standard constructor for the interface `Storable`.
`SimpleParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.parameters.validation

Methods in de.jstacs.parameters.validation that throw NonParsableException
`void` | `StorableValidator.fromXML(StringBuffer representation)` Parses a `StorableValidator` from the XML representation as returned by `StorableValidator.toXML()`.
`void` | `SimpleStaticConstraint.fromXML(StringBuffer representation)` Parses a `SimpleStaticConstraint` from the XML representation as returned by `SimpleStaticConstraint.toXML()`.
`void` | `SimpleReferenceConstraint.fromXML(StringBuffer representation)`
`void` | `ReferenceConstraint.fromXML(StringBuffer representation)` Parses a `ReferenceConstraint` from the XML representation as returned by `ReferenceConstraint.toXML()`.
`void` | `NumberValidator.fromXML(StringBuffer representation)` Parses a `NumberValidator` from the XML representation as returned by `NumberValidator.toXML()`.
`void` | `ConstraintValidator.fromXML(StringBuffer representation)` Parses a `ConstraintValidator` from the XML representation as returned by `ConstraintValidator.toXML()`.

Constructors in de.jstacs.parameters.validation that throw NonParsableException
`ConstraintValidator(StringBuffer representation)` The standard constructor for the interface `Storable`.
`NumberValidator(StringBuffer representation)` The standard constructor for the interface `Storable`.
`ReferenceConstraint(StringBuffer representation)` The standard constructor for the interface `Storable`.
`SimpleReferenceConstraint(StringBuffer representation)` The standard constructor for the interface `Storable`.
`SimpleStaticConstraint(StringBuffer representation)` The standard constructor for the interface `Storable`.
`StorableValidator(StringBuffer buf)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.results

Methods in de.jstacs.results that throw NonParsableException
`protected void` | `Result.extractMainInfo(StringBuffer buf)` This method can be used in the method `Result.fromXML(StringBuffer)` to extract the main information (name, comment, data type).
`protected void` | `StorableResult.fromXML(StringBuffer representation)`
`protected void` | `SimpleResult.fromXML(StringBuffer representation)`
`protected void` | `SampleResult.fromXML(StringBuffer rep)`
`protected void` | `ResultSet.fromXML(StringBuffer representation)` Parses the contents of a `ResultSet` from its XML representation as returned by `ResultSet.toXML()`.
`protected abstract void` | `Result.fromXML(StringBuffer rep)` This method is used in `Result.Result(StringBuffer)` to extract the information.
`protected void` | `NumericalResult.fromXML(StringBuffer representation)`
`protected void` | `MeanResultSet.fromXML(StringBuffer representation)`
`protected void` | `ListResult.fromXML(StringBuffer representation)`
`protected void` | `ImageResult.fromXML(StringBuffer representation)`
`protected void` | `CategoricalResult.fromXML(StringBuffer representation)`

Constructors in de.jstacs.results that throw NonParsableException
`CategoricalResult(StringBuffer representation)` The standard constructor for the interface `Storable`.
`ImageResult(StringBuffer xml)` The standard constructor for the interface `Storable`.
`ListResult(StringBuffer representation)` The standard constructor for the interface `Storable`.
`MeanResultSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`NumericalResult(StringBuffer representation)` The standard constructor for the interface `Storable`.
`NumericalResultSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`Result(StringBuffer rep)` The standard constructor for the interface `Storable`.
`ResultSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`SampleResult(StringBuffer source)` The standard constructor for the interface `Storable`.
`SimpleResult(StringBuffer rep)` This is the constructor for `Storable`.
`StorableResult(StringBuffer buf)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.scoringFunctions

Methods in de.jstacs.scoringFunctions that throw NonParsableException
`protected void` | `UniformScoringFunction.fromXML(StringBuffer xml)`
`protected void` | `NormalizedScoringFunction.fromXML(StringBuffer xml)`
`protected void` | `MRFScoringFunction.fromXML(StringBuffer representation)`
`protected void` | `IndependentProductScoringFunction.fromXML(StringBuffer rep)`
`protected void` | `CMMScoringFunction.fromXML(StringBuffer xml)`
`protected abstract void` | `AbstractNormalizableScoringFunction.fromXML(StringBuffer xml)` This method is called in the constructor for the `Storable` interface to create a scoring function from a `StringBuffer`.

Constructors in de.jstacs.scoringFunctions that throw NonParsableException
`AbstractNormalizableScoringFunction(StringBuffer xml)` This is the constructor for `Storable`.
`AbstractVariableLengthScoringFunction(StringBuffer source)` This is the constructor for the interface `Storable`.
`CMMScoringFunction(StringBuffer source)` This is the constructor for `Storable`.
`IndependentProductScoringFunction(StringBuffer source)` This is the constructor for the interface `Storable`.
`MRFScoringFunction(StringBuffer source)` This is the constructor for the interface `Storable`.
`NormalizedScoringFunction(StringBuffer xml)` This is the constructor for `Storable`.
`UniformScoringFunction(StringBuffer xml)` This is the constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.scoringFunctions.directedGraphicalModels

Methods in de.jstacs.scoringFunctions.directedGraphicalModels that throw NonParsableException
`protected void` | `MutableMarkovModelScoringFunction.fromXML(StringBuffer source)`
`protected void` | `BayesianNetworkScoringFunction.fromXML(StringBuffer source)`

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels that throw NonParsableException
`BayesianNetworkScoringFunction(StringBuffer xml)` The standard constructor for the interface `Storable`.
`BayesianNetworkScoringFunctionParameterSet(StringBuffer representation)` Creates a new `BayesianNetworkScoringFunctionParameterSet` from its XML representation as defined by the `Storable` interface.
`MutableMarkovModelScoringFunction(StringBuffer xml)` The standard constructor for the interface `Storable`.
`Parameter(StringBuffer representation)` The standard constructor for the interface `Storable`.
`ParameterTree.TreeElement(StringBuffer representation)`
`ParameterTree(StringBuffer source)` Recreates a `ParameterTree` from its XML representation as returned by `ParameterTree.toXML()`.

Uses of NonParsableException in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures that throw NonParsableException
`InhomogeneousMarkov.InhomogeneousMarkovParameterSet(StringBuffer representation)` Creates a new `InhomogeneousMarkov.InhomogeneousMarkovParameterSet` from its XML representation as defined by the `Storable` interface.
`InhomogeneousMarkov(StringBuffer buf)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures that throw NonParsableException
`BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .
`BTExplainingAwayResidual(StringBuffer buf)` The standard constructor for the interface `Storable`.
`BTMutualInformation.BTMutualInformationParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .
`BTMutualInformation(StringBuffer buf)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures that throw NonParsableException
`PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet(StringBuffer representation)` Creates a new `PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet` from its XML representation as defined by the `Storable` interface.
`PMMExplainingAwayResidual(StringBuffer buf)` The standard constructor for the interface `Storable`.
`PMMMutualInformation.PMMMutualInformationParameterSet(StringBuffer representation)` Creates a new `PMMMutualInformation.PMMMutualInformationParameterSet` from its XML representation as defined by the `Storable` interface.
`PMMMutualInformation(StringBuffer buf)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.scoringFunctions.homogeneous

Methods in de.jstacs.scoringFunctions.homogeneous that throw NonParsableException
`protected void` | `UniformHomogeneousScoringFunction.fromXML(StringBuffer xml)`
`protected void` | `HMMScoringFunction.fromXML(StringBuffer xml)`
`protected void` | `HMM0ScoringFunction.fromXML(StringBuffer xml)`

Constructors in de.jstacs.scoringFunctions.homogeneous that throw NonParsableException
`HMM0ScoringFunction(StringBuffer xml)` This is the constructor for `Storable`.
`HMMScoringFunction(StringBuffer xml)` This is the constructor for `Storable`.
`HomogeneousScoringFunction(StringBuffer source)` This is the constructor for `Storable`.
`UniformHomogeneousScoringFunction(StringBuffer xml)` This is the constructor for `Storable`.

Uses of NonParsableException in de.jstacs.scoringFunctions.mix

Methods in de.jstacs.scoringFunctions.mix that throw NonParsableException
`protected void` | `StrandScoringFunction.extractFurtherInformation(StringBuffer xml)`
`protected void` | `AbstractMixtureScoringFunction.extractFurtherInformation(StringBuffer xml)` This method is the opposite of `AbstractMixtureScoringFunction.getFurtherInformation()`.
`protected void` | `AbstractMixtureScoringFunction.fromXML(StringBuffer b)`

Constructors in de.jstacs.scoringFunctions.mix that throw NonParsableException
`AbstractMixtureScoringFunction(StringBuffer xml)` This is the constructor for the interface `Storable`.
`MixtureScoringFunction(StringBuffer xml)` This is the constructor for the interface `Storable`.
`StrandScoringFunction(StringBuffer xml)` This is the constructor for `Storable`.
`VariableLengthMixtureScoringFunction(StringBuffer xml)` This is the constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.scoringFunctions.mix.motifSearch

Methods in de.jstacs.scoringFunctions.mix.motifSearch that throw NonParsableException
`protected void` | `HiddenMotifsMixture.extractFurtherInformation(StringBuffer xml)`
`protected void` | `SkewNormalLikeScoringFunction.fromXML(StringBuffer rep)`
`protected void` | `PositionScoringFunction.fromXML(StringBuffer xml)`
`protected void` | `MixtureDuration.fromXML(StringBuffer rep)`
`protected void` | `DurationScoringFunction.fromXML(StringBuffer xml)`

Constructors in de.jstacs.scoringFunctions.mix.motifSearch that throw NonParsableException
`DurationScoringFunction(StringBuffer source)` This is the constructor for `Storable`.
`HiddenMotifsMixture(StringBuffer source)` This is the constructor for the interface `Storable`.
`MixtureDuration(StringBuffer source)` This is the constructor for `Storable`.
`PositionScoringFunction(StringBuffer source)` This is the constructor for `Storable`.
`SkewNormalLikeScoringFunction(StringBuffer source)` This is the constructor for `Storable`.
`UniformDurationScoringFunction(StringBuffer b)` This is the constructor for `Storable`.

Uses of NonParsableException in de.jstacs.utils

Constructors in de.jstacs.utils that throw NonParsableException
`DoubleList(StringBuffer rep)` This is the constructor for the interface `Storable`.

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