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## Uses of Class
de.jstacs.io.NonParsableException

Packages that use NonParsableException
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 `Classifier`s that are based on `SequenceScore`s.
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix | Provides an implementation of a classifier that allows to train the parameters of a set of `DifferentiableStatisticalModel`s 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 `DifferentiableStatisticalModel`s either by maximum supervised posterior (MSP) or by maximum conditional likelihood (MCL)
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling | Provides the classes for `AbstractScoreBasedClassifier`s that are based on `SamplingDifferentiableStatisticalModel`s 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 `Classifier`s that are based on `TrainableStatisticalModel`s
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.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 `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | Provides `DifferentiableStatisticalModel`s 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 `DifferentiableStatisticalModel`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
de.jstacs.sequenceScores.statisticalModels.trainable | Provides all `TrainableStatisticalModel`s, 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 |

Uses of NonParsableException in de.jstacs

Methods in de.jstacs that throw NonParsableException
`protected abstract void` | `AnnotatedEntity.extractFurtherInfos(StringBuffer buf)` This method can be used in the constructor with parameter `StringBuffer` to extract the further information.

Constructors in de.jstacs that throw NonParsableException
`AnnotatedEntity(StringBuffer rep)` The standard constructor for the interface `Storable`.

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.classifiers

Methods in de.jstacs.classifiers 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.extractFurtherInfos(StringBuffer xml)`

Constructors in de.jstacs.classifiers 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`.
`MappingClassifier(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.classifiers.assessment

Constructors in de.jstacs.classifiers.assessment that throw NonParsableException
`ClassifierAssessmentAssessParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`KFoldCrossValidationAssessParameterSet(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.classifiers.differentiableSequenceScoreBased

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

Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased 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.classifiers.differentiableSequenceScoreBased.gendismix

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

Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.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.classifiers.differentiableSequenceScoreBased.logPrior

Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.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.classifiers.differentiableSequenceScoreBased.msp

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

Uses of NonParsableException in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling

Methods in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling that throw NonParsableException
`protected void` | `SamplingScoreBasedClassifier.DiffSMSamplingComponent.createFiles(StringBuffer contents)` Creates files out of file contents saved as XML.
`protected void` | `SamplingScoreBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)`
`protected void` | `SamplingGenDisMixClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)`

Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling that throw NonParsableException
`SamplingGenDisMixClassifier(StringBuffer xml)` Creates a new `SamplingGenDisMixClassifier` from its XML-representation
`SamplingScoreBasedClassifier(StringBuffer xml)` This is the constructor for `Storable`.

Uses of NonParsableException in de.jstacs.classifiers.performanceMeasures

Constructors in de.jstacs.classifiers.performanceMeasures that throw NonParsableException
`AbstractPerformanceMeasure(StringBuffer xml)` The standard constructor for the interface `Storable`.
`AucPR(StringBuffer xml)` The standard constructor for the interface `Storable`.
`AucROC(StringBuffer xml)` The standard constructor for the interface `Storable`.
`ClassificationRate(StringBuffer xml)` The standard constructor for the interface `Storable`.
`ConfusionMatrix(StringBuffer xml)` The standard constructor for the interface `Storable`.
`FalsePositiveRateForFixedSensitivity(StringBuffer xml)` The standard constructor for the interface `Storable`.
`MaximumCorrelationCoefficient(StringBuffer xml)` The standard constructor for the interface `Storable`.
`MaximumFMeasure(StringBuffer xml)` The standard constructor for the interface `Storable`.
`MaximumNumericalTwoClassMeasure(StringBuffer xml)` The standard constructor for the interface `Storable`.
`NumericalPerformanceMeasureParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`PerformanceMeasureParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`PositivePredictiveValueForFixedSensitivity(StringBuffer xml)` The standard constructor for the interface `Storable`.
`PRCurve(StringBuffer xml)` The standard constructor for the interface `Storable`.
`ROCCurve(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SensitivityForFixedSpecificity(StringBuffer xml)` The standard constructor for the interface `Storable`.
`TwoClassAbstractPerformanceMeasure(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.classifiers.trainSMBased

Methods in de.jstacs.classifiers.trainSMBased that throw NonParsableException
`protected void` | `TrainSMBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)`

Constructors in de.jstacs.classifiers.trainSMBased that throw NonParsableException
`TrainSMBasedClassifier(StringBuffer xml)` The standard constructor for the interface `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
`AlphabetContainer.AbstractAlphabetContainerParameterSet(StringBuffer xml)` 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
`Alphabet.AlphabetParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable` .
`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`.
`GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`GenericComplementableDiscreteAlphabet(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.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` | `SimpleParameter.extractFurtherInfos(StringBuffer representation)`
`protected void` | `SelectionParameter.extractFurtherInfos(StringBuffer representation)`
`protected void` | `RangeParameter.extractFurtherInfos(StringBuffer buf)`
`protected void` | `ParameterSetContainer.extractFurtherInfos(StringBuffer representation)`
`protected void` | `Parameter.extractFurtherInfos(StringBuffer source)`
`protected void` | `MultiSelectionParameter.extractFurtherInfos(StringBuffer representation)`
`protected void` | `FileParameter.extractFurtherInfos(StringBuffer buf)`
`protected void` | `EnumParameter.extractFurtherInfos(StringBuffer buf)`
`protected void` | `AbstractSelectionParameter.extractFurtherInfos(StringBuffer representation)`
`protected void` | `SequenceScoringParameterSet.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` | `InstanceParameterSet.fromXML(StringBuffer representation)`
`protected void` | `ExpandableParameterSet.fromXML(StringBuffer representation)`
`protected void` | `ArrayParameterSet.fromXML(StringBuffer representation)`

Constructors in de.jstacs.parameters that throw NonParsableException
`AbstractSelectionParameter(StringBuffer representation)` The standard constructor for the interface `Storable`.
`ArrayParameterSet(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`.
`MultiSelectionParameter(StringBuffer representation)` The standard constructor for the interface `Storable`.
`Parameter(StringBuffer xml)` 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`.
`SelectionParameter(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` | `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`.
`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` | `StorableResult.extractFurtherInfos(StringBuffer representation)`
`protected void` | `SimpleResult.extractFurtherInfos(StringBuffer representation)`
`protected void` | `ListResult.extractFurtherInfos(StringBuffer representation)`
`protected void` | `ImageResult.extractFurtherInfos(StringBuffer representation)`
`protected void` | `DataSetResult.extractFurtherInfos(StringBuffer rep)`
`protected void` | `ResultSet.fromXML(StringBuffer representation)` Parses the contents of a `ResultSet` from its XML representation as returned by `ResultSet.toXML()`.
`protected void` | `MeanResultSet.fromXML(StringBuffer representation)`

Constructors in de.jstacs.results that throw NonParsableException
`CategoricalResult(StringBuffer representation)` The standard constructor for the interface `Storable`.
`DataSetResult(StringBuffer source)` 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`.
`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.sampling

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

Constructors in de.jstacs.sampling that throw NonParsableException
`AbstractBurnInTest(StringBuffer rep)` This is the constructor for the `Storable` interface.
`AbstractBurnInTestParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.
`SimpleBurnInTest(StringBuffer xml)` Deprecated. The standard constructor for the interface `Storable`.
`VarianceRatioBurnInTest(StringBuffer rep)` The standard constructor for the `Storable` interface.
`VarianceRatioBurnInTestParameterSet(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.differentiable

Methods in de.jstacs.sequenceScores.differentiable that throw NonParsableException
`protected void` | `UniformDiffSS.extractFurtherInformation(StringBuffer xml)` This method is the opposite of `UniformDiffSS.getFurtherInformation()`.
`protected void` | `IndependentProductDiffSS.extractFurtherInformation(StringBuffer xml)` This method is the opposite of `IndependentProductDiffSS.getFurtherInformation()`.
`protected void` | `UniformDiffSS.fromXML(StringBuffer xml)`
`protected void` | `IndependentProductDiffSS.fromXML(StringBuffer rep)`
`protected abstract void` | `AbstractDifferentiableSequenceScore.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.sequenceScores.differentiable that throw NonParsableException
`AbstractDifferentiableSequenceScore(StringBuffer xml)` This is the constructor for `Storable`.
`IndependentProductDiffSS(StringBuffer source)` This is the constructor for the interface `Storable`.
`UniformDiffSS(StringBuffer xml)` This is the constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.differentiable.logistic

Methods in de.jstacs.sequenceScores.differentiable.logistic that throw NonParsableException
`protected void` | `LogisticDiffSS.fromXML(StringBuffer xml)`

Constructors in de.jstacs.sequenceScores.differentiable.logistic that throw NonParsableException
`LogisticDiffSS(StringBuffer xml)` This is the constructor for `Storable`.
`ProductConstraint(StringBuffer xml)` This is the constructor for `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable that throw NonParsableException
`protected void` | `UniformDiffSM.extractFurtherInformation(StringBuffer xml)`
`protected void` | `IndependentProductDiffSM.extractFurtherInformation(StringBuffer rep)`
`protected void` | `NormalizedDiffSM.fromXML(StringBuffer xml)`
`protected void` | `MultiDimensionalSequenceWrapperDiffSM.fromXML(StringBuffer xml)`
`protected void` | `MarkovRandomFieldDiffSM.fromXML(StringBuffer representation)`
`protected void` | `MappingDiffSM.fromXML(StringBuffer xml)`
`protected void` | `CyclicMarkovModelDiffSM.fromXML(StringBuffer xml)`

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable that throw NonParsableException
`AbstractDifferentiableStatisticalModel(StringBuffer xml)` This is the constructor for `Storable`.
`AbstractVariableLengthDiffSM(StringBuffer source)` This is the constructor for the interface `Storable`.
`CyclicMarkovModelDiffSM(StringBuffer source)` This is the constructor for `Storable`.
`IndependentProductDiffSM(StringBuffer source)` This is the constructor for the interface `Storable`.
`MappingDiffSM(StringBuffer xml)` This is the constructor for `Storable`.
`MarkovRandomFieldDiffSM(StringBuffer source)` This is the constructor for the interface `Storable`.
`MultiDimensionalSequenceWrapperDiffSM(StringBuffer xml)` This is the constructor for `Storable`.
`NormalizedDiffSM(StringBuffer xml)` This is the constructor for `Storable`.
`UniformDiffSM(StringBuffer xml)` This is the constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels that throw NonParsableException
`protected void` | `MarkovModelDiffSM.fromXML(StringBuffer source)`
`protected void` | `BayesianNetworkDiffSM.fromXML(StringBuffer source)`

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels that throw NonParsableException
`BayesianNetworkDiffSM(StringBuffer xml)` The standard constructor for the interface `Storable`.
`BayesianNetworkDiffSMParameterSet(StringBuffer representation)` Creates a new `BayesianNetworkDiffSMParameterSet` from its XML representation as defined by the `Storable` interface.
`BNDiffSMParameter(StringBuffer representation)` The standard constructor for the interface `Storable`.
`BNDiffSMParameterTree.TreeElement(StringBuffer representation)` Constructor for the `Storable` interface.
`BNDiffSMParameterTree(StringBuffer source)` Recreates a `BNDiffSMParameterTree` from its XML representation as returned by `BNDiffSMParameterTree.toXML()`.
`MarkovModelDiffSM(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.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`.
`Measure.MeasureParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`Measure(StringBuffer xml)` Creates a new `Measure` from its XML-representation.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.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.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.pmmMeasures

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.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.sequenceScores.statisticalModels.differentiable.homogeneous

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous that throw NonParsableException
`protected void` | `UniformHomogeneousDiffSM.fromXML(StringBuffer xml)`
`protected void` | `HomogeneousMMDiffSM.fromXML(StringBuffer xml)`
`protected void` | `HomogeneousMM0DiffSM.fromXML(StringBuffer xml)`

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous that throw NonParsableException
`HomogeneousDiffSM(StringBuffer source)` This is the constructor for `Storable`.
`HomogeneousMM0DiffSM(StringBuffer xml)` This is the constructor for `Storable`.
`HomogeneousMMDiffSM(StringBuffer xml)` This is the constructor for `Storable`.
`UniformHomogeneousDiffSM(StringBuffer xml)` This is the constructor for `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture that throw NonParsableException
`protected void` | `StrandDiffSM.extractFurtherInformation(StringBuffer xml)`
`protected void` | `AbstractMixtureDiffSM.extractFurtherInformation(StringBuffer xml)` This method is the opposite of `AbstractMixtureDiffSM.getFurtherInformation()`.
`protected void` | `AbstractMixtureDiffSM.fromXML(StringBuffer b)`

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture that throw NonParsableException
`AbstractMixtureDiffSM(StringBuffer xml)` This is the constructor for the interface `Storable`.
`MixtureDiffSM(StringBuffer xml)` This is the constructor for the interface `Storable`.
`StrandDiffSM(StringBuffer xml)` This is the constructor for `Storable`.
`VariableLengthMixtureDiffSM(StringBuffer xml)` This is the constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif that throw NonParsableException
`protected void` | `ExtendedZOOPSDiffSM.extractFurtherInformation(StringBuffer xml)`
`protected void` | `SkewNormalLikeDurationDiffSM.fromXML(StringBuffer rep)`
`protected void` | `PositionDiffSM.fromXML(StringBuffer xml)`
`protected void` | `MixtureDurationDiffSM.fromXML(StringBuffer rep)`
`protected void` | `DurationDiffSM.fromXML(StringBuffer xml)`

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif that throw NonParsableException
`DurationDiffSM(StringBuffer source)` This is the constructor for `Storable`.
`ExtendedZOOPSDiffSM(StringBuffer source)` This is the constructor for the interface `Storable`.
`MixtureDurationDiffSM(StringBuffer source)` This is the constructor for `Storable`.
`PositionDiffSM(StringBuffer source)` This is the constructor for `Storable`.
`SkewNormalLikeDurationDiffSM(StringBuffer source)` This is the constructor for `Storable`.
`UniformDurationDiffSM(StringBuffer b)` This is the constructor for `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable

Methods in de.jstacs.sequenceScores.statisticalModels.trainable that throw NonParsableException
`protected void` | `VariableLengthWrapperTrainSM.fromXML(StringBuffer xml)`
`void` | `UniformTrainSM.fromXML(StringBuffer representation)`
`protected void` | `DifferentiableStatisticalModelWrapperTrainSM.fromXML(StringBuffer xml)`
`void` | `CompositeTrainSM.fromXML(StringBuffer representation)`
`protected abstract void` | `AbstractTrainableStatisticalModel.fromXML(StringBuffer xml)` This method should only be used by the constructor that works on a `StringBuffer`.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable that throw NonParsableException
`AbstractTrainableStatisticalModel(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.
`CompositeTrainSM(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.
`DifferentiableStatisticalModelWrapperTrainSM(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.
`UniformTrainSM(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.
`VariableLengthWrapperTrainSM(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.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` | `DiscreteGraphicalTrainSM.fromXML(StringBuffer representation)`
`protected void` | `DiscreteGraphicalTrainSM.set(DGTrainSMParameterSet params, boolean trained)` Sets the parameters as internal parameters and does some essential computations.
`protected abstract void` | `DiscreteGraphicalTrainSM.setFurtherModelInfos(StringBuffer xml)` This method replaces the internal model information with those from a `StringBuffer`.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete that throw NonParsableException
`Constraint(StringBuffer xml)` The standard constructor for the interface `Storable`.
`DGTrainSMParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.
`DiscreteGraphicalTrainSM(DGTrainSMParameterSet params)` The default constructor.
`DiscreteGraphicalTrainSM(StringBuffer representation)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous that throw NonParsableException
`protected void` | `HomogeneousTrainSM.HomCondProb.extractAdditionalInfo(StringBuffer xml)`
`protected void` | `HomogeneousTrainSM.set(DGTrainSMParameterSet params, boolean trained)`
`protected void` | `HomogeneousMM.set(DGTrainSMParameterSet params, boolean trained)`
`protected void` | `HomogeneousMM.setFurtherModelInfos(StringBuffer xml)`

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.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`.
`HomogeneousTrainSM.HomCondProb(StringBuffer xml)` The standard constructor for the interface `Storable` .
`HomogeneousTrainSM(HomogeneousTrainSMParameterSet params)` Creates a homogeneous model from a parameter set.
`HomogeneousTrainSM(StringBuffer stringBuff)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous.parameters

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

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.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` | `InhomogeneousDGTrainSM.set(DGTrainSMParameterSet parameter, boolean trained)`
`protected void` | `FSDAGTrainSM.set(DGTrainSMParameterSet params, boolean trained)`
`protected void` | `BayesianNetworkTrainSM.set(DGTrainSMParameterSet parameter, boolean trained)`
`protected void` | `FSDAGModelForGibbsSampling.setFurtherModelInfos(StringBuffer xml)`
`protected void` | `DAGTrainSM.setFurtherModelInfos(StringBuffer xml)`

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous that throw NonParsableException
`BayesianNetworkTrainSM(BayesianNetworkTrainSMParameterSet params)` Creates a new `BayesianNetworkTrainSM` from a given `BayesianNetworkTrainSMParameterSet`.
`BayesianNetworkTrainSM(StringBuffer representation)` The standard constructor for the interface `Storable`.
`DAGTrainSM(IDGTrainSMParameterSet params)` This is the main constructor.
`DAGTrainSM(StringBuffer xml)` The standard constructor for the interface `Storable`.
`FSDAGModelForGibbsSampling(FSDAGModelForGibbsSamplingParameterSet params)` The default constructor.
`FSDAGModelForGibbsSampling(StringBuffer representation)` This is the constructor for the `Storable` interface.
`FSDAGTrainSM(FSDAGTrainSMParameterSet params)` This is the main constructor.
`FSDAGTrainSM(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`.
`InhomogeneousDGTrainSM(IDGTrainSMParameterSet params)` Creates a new `InhomogeneousDGTrainSM` from a given `IDGTrainSMParameterSet`.
`InhomogeneousDGTrainSM(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.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.parameters that throw NonParsableException
`BayesianNetworkTrainSMParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.
`FSDAGModelForGibbsSamplingParameterSet(StringBuffer s)` The constructor for the `Storable` interface.
`FSDAGTrainSMParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.
`IDGTrainSMParameterSet(StringBuffer s)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared

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

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.hmm

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm that throw NonParsableException
`protected abstract void` | `AbstractHMM.extractFurtherInformation(StringBuffer xml)` This method extracts further information from the XML representation.
`protected void` | `AbstractHMM.fromXML(StringBuffer xml)` This method is used by the `AbstractHMM.AbstractHMM(StringBuffer)` constructor for creating an instance from an XML representation.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm that throw NonParsableException
`AbstractHMM(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models that throw NonParsableException
`protected void` | `SamplingHigherOrderHMM.extractFurtherInformation(StringBuffer xml)`
`protected void` | `HigherOrderHMM.extractFurtherInformation(StringBuffer xml)` This method extracts further information from the XML representation.
`protected void` | `DifferentiableHigherOrderHMM.extractFurtherInformation(StringBuffer xml)`

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models that throw NonParsableException
`DifferentiableHigherOrderHMM(StringBuffer xml)` The standard constructor for the interface `Storable`.
`HigherOrderHMM(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SamplingHigherOrderHMM(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SamplingPhyloHMM(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions that throw NonParsableException
`MixtureEmission(StringBuffer xml)` The standard constructor for the interface `Storable`.
`UniformEmission(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous that throw NonParsableException
`protected void` | `PluginGaussianEmission.fromXML(StringBuffer xml)`
`protected void` | `GaussianEmission.fromXML(StringBuffer xml)` This method is internally used by the constructor `GaussianEmission.GaussianEmission(StringBuffer)`.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous that throw NonParsableException
`GaussianEmission(StringBuffer xml)` Creates a `GaussianEmission` from its XML representation.
`PluginGaussianEmission(StringBuffer xml)` Creates a `PluginGaussianEmission` from its XML representation.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete that throw NonParsableException
`protected void` | `ReferenceSequenceDiscreteEmission.extractFurtherInformation(StringBuffer xml)`
`protected void` | `PhyloDiscreteEmission.extractFurtherInformation(StringBuffer xml)`
`protected void` | `AbstractConditionalDiscreteEmission.extractFurtherInformation(StringBuffer xml)` This method extracts further information from the XML representation.
`protected void` | `AbstractConditionalDiscreteEmission.fromXML(StringBuffer xml)` This method is internally used by the constructor `AbstractConditionalDiscreteEmission.AbstractConditionalDiscreteEmission(StringBuffer)`.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete that throw NonParsableException
`AbstractConditionalDiscreteEmission(StringBuffer xml)` Creates a `AbstractConditionalDiscreteEmission` from its XML representation.
`DiscreteEmission(StringBuffer xml)` Creates a `DiscreteEmission` from its XML representation.
`ReferenceSequenceDiscreteEmission(StringBuffer xml)` Creates a `ReferenceSequenceDiscreteEmission` from its XML representation.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training that throw NonParsableException
`BaumWelchParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`HMMTrainingParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`MaxHMMTrainingParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`MultiThreadedTrainingParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`NumericalHMMTrainingParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`SamplingHMMTrainingParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.
`ViterbiParameterSet(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions that throw NonParsableException
`protected void` | `HigherOrderTransition.extractFurtherInformation(StringBuffer xml)`
`protected void` | `BasicHigherOrderTransition.extractFurtherInformation(StringBuffer xml)` This method extracts further information from the XML representation.
`protected abstract void` | `BasicHigherOrderTransition.AbstractTransitionElement.extractFurtherInformation(StringBuffer xml)` This method extracts further information from the XML representation.

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions that throw NonParsableException
`BasicHigherOrderTransition.AbstractTransitionElement(StringBuffer xml)` The standard constructor for the interface `Storable`.
`BasicHigherOrderTransition(StringBuffer xml)` The standard constructor for the interface `Storable`.
`HigherOrderTransition(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements that throw NonParsableException
`protected void` | `ScaledTransitionElement.extractFurtherInformation(StringBuffer xml)`
`protected void` | `ReferenceBasedTransitionElement.extractFurtherInformation(StringBuffer xml)`
`protected void` | `DistanceBasedScaledTransitionElement.extractFurtherInformation(StringBuffer xml)`
`protected void` | `BasicTransitionElement.extractFurtherInformation(StringBuffer xml)`
`protected void` | `BasicPluginTransitionElement.extractFurtherInformation(StringBuffer xml)`

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements that throw NonParsableException
`BasicPluginTransitionElement(StringBuffer xml)` The standard constructor for the interface `Storable`.
`BasicTransitionElement(StringBuffer xml)` The standard constructor for the interface `Storable`.
`DistanceBasedScaledTransitionElement(StringBuffer xml)` Extracts a distance-base scaled transition element from XML.
`ReferenceBasedTransitionElement(StringBuffer xml)` The standard constructor for the interface `Storable`.
`ScaledTransitionElement(StringBuffer xml)` The standard constructor for the interface `Storable`.
`TransitionElement(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.mixture

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture that throw NonParsableException
`protected void` | `AbstractMixtureTrainSM.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` | `AbstractMixtureTrainSM.fromXML(StringBuffer representation)`

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.mixture that throw NonParsableException
`AbstractMixtureTrainSM(StringBuffer xml)` The standard constructor for the interface `Storable`.
`MixtureTrainSM(StringBuffer xml)` The constructor for the interface `Storable`.
`StrandTrainSM(StringBuffer stringBuff)` The constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif

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

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif that throw NonParsableException
`HiddenMotifMixture(StringBuffer xml)` The standard constructor for the interface `Storable`.
`ZOOPSTrainSM(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.phylo

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.phylo that throw NonParsableException
`PhyloNode(StringBuffer xml)` The standard constructor for the interface `Storable`.
`PhyloTree(StringBuffer xml)` The standard constructor for the interface `Storable`.

Uses of NonParsableException in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.phylo.parser that throw NonParsableException
`PhyloTree` | `NewickParser.tokenize()` This method construct a `PhyloTree` from the given input stream

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`.

Uses of NonParsableException in de.jstacs.utils.galaxy

Methods in de.jstacs.utils.galaxy that throw NonParsableException
`protected void` | `GalaxyAdaptor.LinkedImageResult.extractFurtherInfos(StringBuffer representation)`
`protected void` | `GalaxyAdaptor.FileResult.extractFurtherInfos(StringBuffer rep)`

Constructors in de.jstacs.utils.galaxy that throw NonParsableException
`GalaxyAdaptor.FileResult(StringBuffer rep)` Creates a new `GalaxyAdaptor.FileResult` from its XML-representation
`GalaxyAdaptor.LinkedImageResult(StringBuffer xml)` Creates a new `GalaxyAdaptor.LinkedImageResult` from its XML-representation

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