Uses of Class
de.jstacs.io.NonParsableException

Packages that use NonParsableException

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

Uses of NonParsableException in de.jstacs

Methods in de.jstacs that throw NonParsableException

Modifier and Type	Method and Description
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

Constructor and Description
AnnotatedEntity(StringBuffer rep) The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.algorithms.alignment

Methods in de.jstacs.algorithms.alignment that throw NonParsableException

Modifier and Type	Method and Description
protected void	StringAlignment.fromXML(StringBuffer xml) Parses the XML representation.
protected void	PairwiseStringAlignment.fromXML(StringBuffer xml)

Constructors in de.jstacs.algorithms.alignment that throw NonParsableException

Constructor and Description
PairwiseStringAlignment(StringBuffer xml) The standard constructor for the interface Storable.
StringAlignment(StringBuffer xml) Restores StringAlignment object from its XML representation.

Uses of NonParsableException in de.jstacs.algorithms.alignment.cost

Constructors in de.jstacs.algorithms.alignment.cost that throw NonParsableException

Constructor and Description
AffineCosts(StringBuffer xml) Restores AffineCosts object from its XML representation.
MatrixCosts(StringBuffer xml) Restores MatrixCosts object from its XML representation.
SimpleCosts(StringBuffer xml) Restores SimpleCosts object from its XML representation.

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

Constructors in de.jstacs.algorithms.optimization.termination that throw NonParsableException

Constructor and Description
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.
MultipleIterationsCondition.MultipleIterationsConditionParameterSet(StringBuffer xml) The standard constructor for the interface Storable.
MultipleIterationsCondition(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

Modifier and Type	Method and Description
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

Constructor and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
protected void	ScoreClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)

Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased that throw NonParsableException

Constructor and Description
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

Modifier and Type	Method and Description
protected void	GenDisMixClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)

Constructors in de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix that throw NonParsableException

Constructor and Description
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

Constructor and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Constructor and Description
AbstractNumericalTwoClassPerformanceMeasure(StringBuffer xml) The standard constructor for the interface Storable.
AbstractPerformanceMeasure(StringBuffer xml) The standard constructor for the interface Storable.
AbstractPerformanceMeasureParameterSet(StringBuffer xml) The standard constructor for the interface Storable.
AbstractTwoClassPerformanceMeasure(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.

Uses of NonParsableException in de.jstacs.classifiers.trainSMBased

Methods in de.jstacs.classifiers.trainSMBased that throw NonParsableException

Modifier and Type	Method and Description
protected void	TrainSMBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)

Constructors in de.jstacs.classifiers.trainSMBased that throw NonParsableException

Constructor and Description
TrainSMBasedClassifier(StringBuffer xml) The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.clustering.hierachical

Constructors in de.jstacs.clustering.hierachical that throw NonParsableException

Constructor and Description
ClusterTree(StringBuffer xml) Creates a cluster tree from its XML representation

Uses of NonParsableException in de.jstacs.data

Methods in de.jstacs.data that throw NonParsableException

Modifier and Type	Method and Description
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

Constructor and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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 Sequence[]	XMLParser.extractSequencesWithTags(StringBuffer xml, String tag) Extracts a set of sequences from their XML representation.
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
protected void	TextResult.extractFurtherInfos(StringBuffer buf)
protected void	StorableResult.extractFurtherInfos(StringBuffer representation)
protected void	SimpleResult.extractFurtherInfos(StringBuffer representation)
protected void	PlotGeneratorResult.extractFurtherInfos(StringBuffer buf)
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

Constructor and Description
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.
PlotGeneratorResult(StringBuffer rep) Creates a new PlotGeneratorResult from its XML representation.
Result(StringBuffer rep) The standard constructor for the interface Storable.
ResultSet(StringBuffer representation) The standard constructor for the interface Storable.
ResultSetResult(StringBuffer representation) Creates a ResultSetResult from its XML representation.
SimpleResult(StringBuffer rep) This is the constructor for Storable.
StorableResult(StringBuffer buf) The standard constructor for the interface Storable.
TextResult(StringBuffer xml) Creates a TextResult from its XML representation.

Uses of NonParsableException in de.jstacs.sampling

Methods in de.jstacs.sampling that throw NonParsableException

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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	MultiDimensionalSequenceWrapperDiffSS.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

Constructor and Description
AbstractDifferentiableSequenceScore(StringBuffer xml) This is the constructor for Storable.
IndependentProductDiffSS(StringBuffer source) This is the constructor for the interface Storable.
MultiDimensionalSequenceWrapperDiffSS(StringBuffer xml) This is the constructor for 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

Modifier and Type	Method and Description
protected void	LogisticDiffSS.fromXML(StringBuffer xml)

Constructors in de.jstacs.sequenceScores.differentiable.logistic that throw NonParsableException

Constructor and Description
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

Modifier and Type	Method and Description
protected void	UniformDiffSM.extractFurtherInformation(StringBuffer xml)
protected void	IndependentProductDiffSM.extractFurtherInformation(StringBuffer rep)
protected void	NormalizedDiffSM.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

Constructor and Description
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.
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

Modifier and Type	Method and Description
protected void	MarkovModelDiffSM.fromXML(StringBuffer source)
protected void	BayesianNetworkDiffSM.fromXML(StringBuffer source)

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels that throw NonParsableException

Constructor and Description
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

Constructor and Description
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

Constructor and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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.localMixture

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture that throw NonParsableException

Modifier and Type	Method and Description
protected void	LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder.fromXML(StringBuffer xml)

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture that throw NonParsableException

Constructor and Description
LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder(StringBuffer xml) Creates a LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder model from its XML representation

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

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture that throw NonParsableException

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
protected void	VariableLengthWrapperTrainSM.fromXML(StringBuffer xml)
void	UniformTrainSM.fromXML(StringBuffer representation)
protected void	PFMWrapperTrainSM.fromXML(StringBuffer xml)
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

Constructor and Description
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.
PFMWrapperTrainSM(StringBuffer stringBuff) Creates a wrapper from its XML representation
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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	FSMEManager.set(DGTrainSMParameterSet params, boolean trained)
protected void	FSDAGTrainSM.set(DGTrainSMParameterSet params, boolean trained)
protected void	BayesianNetworkTrainSM.set(DGTrainSMParameterSet parameter, boolean trained)
protected void	MEManager.setFurtherModelInfos(StringBuffer xml)
protected void	FSDAGModelForGibbsSampling.setFurtherModelInfos(StringBuffer xml)
protected void	DAGTrainSM.setFurtherModelInfos(StringBuffer xml)

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous that throw NonParsableException

Constructor and Description
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.
FSMEManager(FSMEMParameterSet params) Creates a new MEManager from a given MEManagerParameterSet.
FSMEManager(StringBuffer stringBuff) 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.
MEM(StringBuffer representation) The constructor for the Storable interface.
MEManager(MEManagerParameterSet params) Creates a new MEManager from a given MEManagerParameterSet.
MEManager(StringBuffer stringBuff) 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

Constructor and Description
BayesianNetworkTrainSMParameterSet(StringBuffer s) The standard constructor for the interface Storable.
ConstraintParameterSet(StringBuffer xml) The constructor for the Storable interface.
FSDAGModelForGibbsSamplingParameterSet(StringBuffer s) The constructor for the Storable interface.
FSDAGTrainSMParameterSet(StringBuffer s) The standard constructor for the interface Storable.
FSMEMParameterSet(StringBuffer s) The constructor for the Storable interface.
IDGTrainSMParameterSet(StringBuffer s) The standard constructor for the interface Storable.
MEManagerParameterSet(StringBuffer s) The constructor for the Storable interface.

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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
protected void	PluginGaussianEmission.fromXML(StringBuffer xml)
protected void	MultivariateGaussianEmission.fromXML(StringBuffer xml) Parses the XML representation.
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

Constructor and Description
GaussianEmission(StringBuffer xml) Creates a GaussianEmission from its XML representation.
MultivariateGaussianEmission(StringBuffer xml) Creates a MultivariateGaussianEmission 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

Modifier and Type	Method and Description
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

Constructor and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
protected void	HiddenMotifMixture.extractFurtherInformation(StringBuffer xml)

Constructors in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif that throw NonParsableException

Constructor and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
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

Constructor and Description
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

Modifier and Type	Method and Description
PhyloTree	NewickParser.tokenize() This method construct a PhyloTree from the given input stream

Uses of NonParsableException in de.jstacs.tools

Methods in de.jstacs.tools that throw NonParsableException

Modifier and Type	Method and Description
protected void	ToolResult.extractFurtherInfos(StringBuffer representation)
protected void	DataColumnParameter.extractFurtherInfos(StringBuffer representation)

Constructors in de.jstacs.tools that throw NonParsableException

Constructor and Description
DataColumnParameter(StringBuffer representation) The standard constructor for the interface Storable.
ToolResult(StringBuffer representation) The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.tools.ui.galaxy

Methods in de.jstacs.tools.ui.galaxy that throw NonParsableException

Modifier and Type	Method and Description
protected void	GalaxyAdaptor.LinkedImageResult.extractFurtherInfos(StringBuffer representation)
protected void	GalaxyAdaptor.FileResult.extractFurtherInfos(StringBuffer rep)

Constructors in de.jstacs.tools.ui.galaxy that throw NonParsableException

Constructor and Description
GalaxyAdaptor.FileResult(StringBuffer rep) Creates a new TextResult from its XML-representation
GalaxyAdaptor.LinkedImageResult(StringBuffer xml) Creates a new GalaxyAdaptor.LinkedImageResult from its XML-representation
MultilineSimpleParameter(StringBuffer representation) The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.utils

Constructors in de.jstacs.utils that throw NonParsableException

Constructor and Description
DoubleList(StringBuffer rep) This is the constructor for the interface Storable.
SeqLogoPlotter.SeqLogoPlotGenerator(StringBuffer xml) Creates a SeqLogoPlotter.SeqLogoPlotGenerator from its XML representation.