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## Uses of Class
de.jstacs.NonParsableException

Packages that use NonParsableException
de.jstacs.classifier | This package provides the framework for any classifier.
de.jstacs.classifier.assessment | This package allows to assess classifiers.
de.jstacs.classifier.modelBased | Provides the classes for `Classifier`s that are based on `Model`s
de.jstacs.classifier.scoringFunctionBased | Provides the classes for `Classifier`s that are based on `ScoringFunction`s.
de.jstacs.classifier.scoringFunctionBased.cll | Provides the implementation of the log conditional likelihood as an `OptimizableFunction` and a classifier that uses log conditional likelihood or supervised posterior to learn the parameters of a set of `ScoringFunctions`
de.jstacs.classifier.scoringFunctionBased.logPrior | Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors
de.jstacs.data | Provides classes for the representation of data.
de.jstacs.data.alphabets | Provides classes for the representation of discrete and continuous alphabets, including a `DNAAlphabet` for the most common case of DNA-sequences
de.jstacs.data.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.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.utils | This package contains a bundle of useful classes and interfaces like ...

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 constructor for the `Storable` interface.
`AbstractScoreBasedClassifier.DoubleTableResult(StringBuffer representation)` This is the constructor for the interface `Storable`.
`AbstractScoreBasedClassifier(StringBuffer xml)` The constructor for the `Storable` interface.
`ConfusionMatrix(StringBuffer representation)` This is the constructor for the interface `Storable`.
`MappingClassifier(StringBuffer representation)` This is the constructor for the interface `Storable`.
`MeasureParameters(StringBuffer representation)` Recreates a `MeasureParameters` instance from its XML representation as returned by `MultiSelectionCollectionParameter.toXML()`.

Uses of NonParsableException in de.jstacs.classifier.assessment

Constructors in de.jstacs.classifier.assessment that throw NonParsableException
`ClassifierAssessmentAssessParameterSet(StringBuffer representation)` Constructs a `ClassifierAssessmentAssessParameterSet` out of an XML representation.
`KFoldCVAssessParameterSet(StringBuffer representation)` Constructs a `KFoldCVAssessParameterSet` out of an XML representation.
`RepeatedHoldOutAssessParameterSet(StringBuffer representation)` Constructs a `RepeatedHoldOutAssessParameterSet` out of an XML representation.
`RepeatedSubSamplingAssessParameterSet(StringBuffer representation)` Constructs a `RepeatedSubSamplingAssessParameterSet` out of an XML representation.
`Sampled_RepeatedHoldOutAssessParameterSet(StringBuffer representation)` Constructs a `Sampled_RepeatedHoldOutAssessParameterSet` out of an XML representation.

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)` This is the 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)` This is the constructor for the interface `Storable`.
`ScoreClassifierParameterSet(StringBuffer xml)` This is the constructor for `Storable`.

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

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

Constructors in de.jstacs.classifier.scoringFunctionBased.cll that throw NonParsableException
`CLLClassifier(StringBuffer xml)` This is the constructor for the interface `Storable`.
`CLLClassifierParameterSet(StringBuffer xml)` This is the constructor for `Storable`.

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

Constructors in de.jstacs.classifier.scoringFunctionBased.logPrior that throw NonParsableException
`SeparateGaussianLogPrior(StringBuffer xml)` Recreates a `SeparateGaussianLogPrior` from its XML representation as returned by `SeparateLogPrior.toXML()`.
`SeparateLaplaceLogPrior(StringBuffer xml)` Recreates a `SeparateLaplaceLogPrior` from its XML representation as returned by `SeparateLogPrior.toXML()`.
`SeparateLogPrior(StringBuffer xml)` Recreates a `SeparateLogPrior` from its XML representation as returned by `SeparateLogPrior.toXML()`.
`SimpleGaussianSumLogPrior(StringBuffer xml)` Recreates a `SimpleGaussianSumLogPrior` from its XML representation as returned by `SimpleGaussianSumLogPrior.toXML()`.

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)` Creates a new `Alphabet.AlphabetParameterSet` from its XML representation.
`AlphabetContainer(StringBuffer xml)` Extracts the `AlphabetContainerParameterSet` from a `StringBuffer`.
`AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)` Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from its XML representation.
`AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer representation)` Creates a new `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` from its XML representation.
`AlphabetContainerParameterSet(StringBuffer representation)` Creates a new `AlphabetContainerParameterSet` from its XML representation.

Uses of NonParsableException in de.jstacs.data.alphabets

Constructors in de.jstacs.data.alphabets that throw NonParsableException
`ComplementableDiscreteAlphabet(StringBuffer representation)` The constructor for the `Storable` interface.
`ContinuousAlphabet.ContinuousAlphabetParameterSet(StringBuffer representation)` Creates a new `ContinuousAlphabet.ContinuousAlphabetParameterSet` from its XML representation.
`ContinuousAlphabet(StringBuffer xml)` Extracts the alphabet from the `StringBuffer`.
`DiscreteAlphabet.DiscreteAlphabetParameterSet(StringBuffer representation)` Creates a new `DiscreteAlphabet.DiscreteAlphabetParameterSet` from its XML representation.
`DiscreteAlphabet(StringBuffer representation)` Extracts the alphabet from the `StringBuffer`.
`DNAAlphabet.DNAAlphabetParameterSet(StringBuffer representation)` Creates a new `DNAAlphabet.DNAAlphabetParameterSet` from its XML representation.
`DNAAlphabet(StringBuffer representation)` The constructor for the `Storable` interface.

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)` Re-creates a `CisRegulatoryModuleAnnotation` from its XML representation as returned by `SequenceAnnotation.toXML()`.
`IntronAnnotation(StringBuffer representation)` Re-creates an `IntronAnnotation` from its XML representation as returned by `LocatedSequenceAnnotationWithLength.toXML()`.
`LocatedSequenceAnnotation(StringBuffer representation)` Re-creates a `LocatedSequenceAnnotation` from its XML representation as returned by `LocatedSequenceAnnotation.toXML()`.
`LocatedSequenceAnnotationWithLength(StringBuffer representation)` Re-creates a `LocatedSequenceAnnotationWithLength` from its XML representation as returned by `LocatedSequenceAnnotationWithLength.toXML()`.
`MotifAnnotation(StringBuffer representation)` Re-creates a `MotifAnnotation` from its XML representation as returned by `StrandedLocatedSequenceAnnotationWithLength.toXML()`.
`SequenceAnnotation(StringBuffer representation)` Re-creates a `SequenceAnnotation` from its XML representation as returned by `SequenceAnnotation.toXML()`.
`SinglePositionSequenceAnnotation(StringBuffer representation)` Re-creates a `SinglePositionSequenceAnnotation` from its XML representation as returned by `LocatedSequenceAnnotation.toXML()`.
`StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation)` Re-creates a `StrandedLocatedSequenceAnnotationWithLength` from its XML representation as returned by `StrandedLocatedSequenceAnnotationWithLength.toXML()`.

Uses of NonParsableException in de.jstacs.io

Methods in de.jstacs.io that throw NonParsableException
`static boolean[][]` | `XMLParser.extractBoolean2ArrayForTag(StringBuffer source, String tag)` Returns the value between equal start and end tags as a two dimensional boolean array.
`static boolean[][]` | `XMLParser.extractBoolean2ArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a two dimensional boolean array.
`static boolean[]` | `XMLParser.extractBooleanArrayForTag(StringBuffer source, String tag)` Returns the value between equal start and end tags as a boolean array.
`static boolean[]` | `XMLParser.extractBooleanArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a boolean array.
`static boolean` | `XMLParser.extractBooleanForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as boolean.
`static boolean` | `XMLParser.extractBooleanForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as boolean.
`static byte[][]` | `XMLParser.extractByte2ArrayForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as a two dimensional byte array.
`static byte[][]` | `XMLParser.extractByte2ArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a two dimensional byte array.
`static byte[]` | `XMLParser.extractByteArrayForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as a byte array.
`static byte[]` | `XMLParser.extractByteArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a byte array.
`static byte` | `XMLParser.extractByteForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as byte.
`static byte` | `XMLParser.extractByteForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as byte.
`static double[][]` | `XMLParser.extractDouble2ArrayForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as a two dimensional double array.
`static double[][]` | `XMLParser.extractDouble2ArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a two dimensional double array.
`static double[]` | `XMLParser.extractDoubleArrayForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as a double array.
`static double[]` | `XMLParser.extractDoubleArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a double array.
`static double` | `XMLParser.extractDoubleForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as double.
`static double` | `XMLParser.extractDoubleForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as double.
`static
`<T extends Enum<T>> T`
` | `XMLParser.extractEnumForTag(StringBuffer source, String tag)` Returns the enumeration between equal start and end tags as Enum.
`static
`<T extends Enum<T>> T`
` | `XMLParser.extractEnumForTag(StringBuffer source, String startTag, String endTag)` Returns the enumeration between start and end tag as Enum.
`static StringBuffer` | `XMLParser.extractForTag(StringBuffer source, String tag)` Extracts the code between equal start and end tags and returns the substring between the tags as new StringBuffer.
`static StringBuffer` | `XMLParser.extractForTag(StringBuffer source, String startTag, String endTag)` Returns the substring between start and end tag as StringBuffer.
`static int[][]` | `XMLParser.extractInt2ArrayForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as a two dimensional int array.
`static int[][]` | `XMLParser.extractInt2ArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a two dimensional int array.
`static int[]` | `XMLParser.extractIntArrayForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as an int array.
`static int[]` | `XMLParser.extractIntArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as an int array.
`static int` | `XMLParser.extractIntForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as int.
`static int` | `XMLParser.extractIntForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as int.
`static long` | `XMLParser.extractLongForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as long.
`static long` | `XMLParser.extractLongForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as long.
`static Storable[][]` | `XMLParser.extractStorable2ArrayForTag(StringBuffer source, String tag)` Returns the value between equal start and end tags as a two dimensional `Storable` array.
`static Storable[][]` | `XMLParser.extractStorable2ArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a two dimensional `Storable` array.
`static Storable[][][]` | `XMLParser.extractStorable3ArrayForTag(StringBuffer source, String tag)` Returns the value between equal start and end tags as a three dimensional `Storable` array.
`static Storable[][][]` | `XMLParser.extractStorable3ArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a three dimensional `Storable` array.
`static Storable[]` | `XMLParser.extractStorableArrayForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as a Storable array.
`static Storable[]` | `XMLParser.extractStorableArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a Storable array.
`static Storable` | `XMLParser.extractStorableForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as `Storable`.
`static Storable` | `XMLParser.extractStorableForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as `Storable`.
`static Storable` | `XMLParser.extractStorableOrNullForTag(StringBuffer source, String tag)` Returns the value between equal start and end tags as `Storable` or `null`.
`static Storable` | `XMLParser.extractStorableOrNullForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as `Storable` or `null`.
`static String[][]` | `XMLParser.extractString2ArrayForTag(StringBuffer source, String tag)` Returns the value between equal start and end tags as a two dimensional String array.
`static String[][]` | `XMLParser.extractString2ArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a two dimensional String array.
`static String[]` | `XMLParser.extractStringArrayForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as a String array.
`static String[]` | `XMLParser.extractStringArrayForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a String array.
`static String` | `XMLParser.extractStringForTag(StringBuffer source, String startTag)` Returns the value between equal start and end tags as a String.
`static String` | `XMLParser.extractStringForTag(StringBuffer source, String startTag, String endTag)` Returns the value between start and end tag as a String.

Uses of NonParsableException in de.jstacs.models

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

Constructors in de.jstacs.models that throw NonParsableException
`AbstractModel(StringBuffer stringBuff)` Constructor for parsing a AbstractModel out of a StringBuffer.
`CompositeModel(StringBuffer stringBuff)` The constructor for the `Storable` interface.
`UniformModel(StringBuffer stringBuff)` The constructor for the `Storable` interface.

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 are 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 infos with those from the StringBuffer.

Constructors in de.jstacs.models.discrete that throw NonParsableException
`Constraint(StringBuffer xml)` The constructor for creating an object from an StringBuffer.
`DGMParameterSet(StringBuffer s)` The constructor for the `Storable` interface.
`DiscreteGraphicalModel(DGMParameterSet params)` The default constructor.
`DiscreteGraphicalModel(StringBuffer representation)` The constructor for a model in xml format.

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 homogeneous Markov model from a parameter set.
`HomogeneousMM(StringBuffer stringBuff)` Creates a homogeneous Markov model from a StringBuffer.
`HomogeneousModel.HomCondProb(StringBuffer xml)` Creates an instance from a StringBuffer (see `Storable`).
`HomogeneousModel(HomogeneousModelParameterSet params)` Creates a homogeneous model from a parameter set.
`HomogeneousModel(StringBuffer stringBuff)` Creates a homogeneous model from a StringBuffer.

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 constructor for the `Storable` interface.
`HomogeneousModelParameterSet(StringBuffer s)` The constructor for the `Storable` interface.

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)` The default constructor.
`BayesianNetworkModel(StringBuffer representation)` The constructor for a model in xml format.
`DAGModel(IDGMParameterSet params)` This is the main constructor.
`DAGModel(StringBuffer xml)` This is the constructor for `Storable`.
`FSDAGModel(FSDAGMParameterSet params)` This is the main constructor.
`FSDAGModel(StringBuffer xml)` This is the constructor for `Storable`.
`InhCondProb(StringBuffer xml)` The constructor for saved objects.
`InhConstraint(StringBuffer xml)` The constructor for saved objects.
`InhomogeneousDGM(IDGMParameterSet params)` The default constructor.
`InhomogeneousDGM(StringBuffer representation)` This is the constructor for `Storable`.
`MEMConstraint(StringBuffer xml)` Creates a MEMConstraint from a StringBuffer

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 constructor for the `Storable` interface.
`FSDAGMParameterSet(StringBuffer s)` The constructor for the `Storable` interface.
`IDGMParameterSet(StringBuffer s)` The constructor for the `Storable` interface.

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 constructor for the `Storable` interface.
`SharedStructureMixture(StringBuffer xml)` The constructor for the `Storable` interface.

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)` This constructor can be used for loading a `StrandModel` form a `StringBuffer`;

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 interface `Storable`.
`FSDAGModelForGibbsSampling(FSDAGModelForGibbsSamplingParameterSet params)` The default constructor.
`FSDAGModelForGibbsSampling(StringBuffer representation)` This is the constructor for the interface `Storable`.
`FSDAGModelForGibbsSamplingParameterSet(StringBuffer s)` The constructor for the `Storable` interface.
`SimpleBurnInTest(StringBuffer xml)` The standard constructor for the interface `Storable`.
`VarianceRatioBurnInTest(StringBuffer rep)` The standard constructor for the interface `Storable`.

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 the 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.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 an 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)` Creates a new `ArrayParameterSet` from its XML-representation.
`CollectionParameter(StringBuffer representation)` Restores an instance of `CollectionParameter` from a string representation
`EnumParameter(StringBuffer representation)` Restores an instance of `EnumParameter` from a string representation
`ExpandableParameterSet(StringBuffer representation)` Creates a new `ExpandableParameterSet` from its XML-representation.
`FileParameter.FileRepresentation(StringBuffer buf)` Restores the file representation from an XML representation
`FileParameter(StringBuffer buf)` Restores a file parameter from an XML representation.
`InstanceParameterSet(StringBuffer representation)` Constructs a `InstanceParameterSet` out of an XML representation
`MultiSelectionCollectionParameter(StringBuffer representation)` Creates a new `MultiSelectionCollectionParameter` from its XML-representation
`ParameterSet(StringBuffer representation)` Constructs a `ParameterSet` out of an XML representation
`ParameterSetContainer(StringBuffer representation)` Creates a new `ParameterSetContainer` from its XML-representation.
`RangeParameter(StringBuffer representation)` Restores a `RangeParameter` from its XML-representation.
`SequenceScoringParameterSet(StringBuffer representation)` Constructs a `InstanceParameterSet` from its XML-representation.
`SimpleParameter(StringBuffer representation)` Constructs a `SimpleParameter` out of an XML representation
`SimpleParameterSet(StringBuffer representation)` Constructs a `SimpleParameterSet` from its XML-representation

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)` Creates a new `ConstraintValidator` from its XML-representation.
`NumberValidator(StringBuffer representation)` Constructs a NumberValidator out of a XML representation
`ReferenceConstraint(StringBuffer representation)` Creates a new `ReferenceConstraint` from its XML-representation.
`SimpleReferenceConstraint(StringBuffer representation)` Creates a new `SimpleReferenceConstraint` from its XML-representation.
`SimpleStaticConstraint(StringBuffer representation)` Creates a new `SimpleStaticConstraint` from its XML-representation
`StorableValidator(StringBuffer buf)` Constructs an `ObjectValidator` from its XML-representation

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 fromXML-method to extract the main information (name, comment, datatype).
`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)` Creates a new `CategoricalResult` from its XML-representation.
`ListResult(StringBuffer representation)` Creates a new `ListResult` from the corresponding XML-representation.
`MeanResultSet(StringBuffer representation)` The constructor for a model in xml format.
`NumericalResult(StringBuffer representation)` Constructs a `NumericalResult` from its XML-representation.
`NumericalResultSet(StringBuffer representation)` This is the constructor for `Storable`.
`Result(StringBuffer rep)` The constructor for the Storable interface.
`ResultSet(StringBuffer representation)` Constructs a `ResultSet` from its XML-representation.
`SampleResult(StringBuffer source)` Re-creates a `SampleResult` from its XML-representation as returned by `SampleResult.toXML()`.
`SimpleResult(StringBuffer rep)` This is the constructor for `Storable`.
`StorableResult(StringBuffer buf)` Constructs a new `ObjectResult` from its XML-representation

Uses of NonParsableException in de.jstacs.scoringFunctions

Methods in de.jstacs.scoringFunctions that throw NonParsableException
`protected void` | `UniformScoringFunction.fromXML(StringBuffer xml)`
`protected void` | `MRFScoringFunction.fromXML(StringBuffer representation)`
`protected void` | `IndependentProductScoringFunction.fromXML(StringBuffer rep)`
`protected abstract void` | `AbstractNormalizableScoringFunction.fromXML(StringBuffer xml)` This method is called in the constructor 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`.
`IndependentProductScoringFunction(StringBuffer source)` This is the constructor for `Storable`.
`MRFScoringFunction(StringBuffer source)` This is the constructor for `Storable`.
`UniformScoringFunction(StringBuffer xml)` This is the constructor for `Storable`.
`VariableLengthScoringFunction(StringBuffer source)` This is the constructor for `Storable`.

Uses of NonParsableException in de.jstacs.scoringFunctions.directedGraphicalModels

Methods in de.jstacs.scoringFunctions.directedGraphicalModels that throw NonParsableException
`static ParameterTree[]` | `ParameterTree.fromStringArray(String[] strs, AlphabetContainer alphabet)` Re-creates an array of `ParameterTree`s from their XML-representation as given in `strs`.
`protected void` | `BayesianNetworkScoringFunction.fromXML(StringBuffer source)`

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels that throw NonParsableException
`BayesianNetworkScoringFunction(StringBuffer xml)` Re-creates a BayesianNetworkScoringFunction from its XML-representation, as saved by the `BayesianNetworkScoringFunction.toXML()`} method.
`BayesianNetworkScoringFunctionParameterSet(StringBuffer representation)` Creates a new `BayesianNetworkScoringFunctionParameterSet` from its XML-representation as defined by the `Storable` interface.
`Parameter(StringBuffer representation)` Re-creates a parameter from its XML-representation as returned by the `Parameter.toXML()`} method.
`ParameterTree(StringBuffer source, AlphabetContainer alphabet)` Re-creates 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)` Re-creates an `InhomogeneousMarkov` structure from its XML-representation as returned by `InhomogeneousMarkov.toXML()`.

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)` Creates a new `BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet` from its XML-representation as defined by the `Storable` interface.
`BTExplainingAwayResidual(StringBuffer buf)` Re-creates a `BTExplainingAwayResidual` from is XML-representation as returned by `BTExplainingAwayResidual.toXML()`.
`BTMutualInformation.BTMutualInformationParameterSet(StringBuffer representation)` Creates a new `BTMutualInformation.BTMutualInformationParameterSet` from its XML-representation as defined by the `Storable` interface.
`BTMutualInformation(StringBuffer buf)` Re-creates a `BTMutualInformation` from is XML-representation as returned by `BTMutualInformation.toXML()`.

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)` Re-creates a `PMMExplainingAwayResidual` from its XML-representation as returned by `PMMExplainingAwayResidual.toXML()`.
`PMMMutualInformation.PMMMutualInformationParameterSet(StringBuffer representation)` Creates a new `PMMMutualInformation.PMMMutualInformationParameterSet` from its XML-representation as defined by the `Storable` interface.
`PMMMutualInformation(StringBuffer buf)` Re-creates a `PMMMutualInformation` from its XML-representation as returned by `PMMMutualInformation.toXML()`.

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` | `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 `Storable`.
`MixtureScoringFunction(StringBuffer xml)` 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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