Uses of Class
de.jstacs.NonParsableException

Packages that use NonParsableException

de.jstacs.algorithms.optimization.termination
de.jstacs.classifier	This package provides the framework for any classifier.
de.jstacs.classifier.assessment	This package allows to assess classifiers.
de.jstacs.classifier.modelBased	Provides the classes for Classifiers that are based on Models
de.jstacs.classifier.scoringFunctionBased	Provides the classes for Classifiers that are based on ScoringFunctions.
de.jstacs.classifier.scoringFunctionBased.gendismix	Provides an implementation of a classifier that allows to train the parameters of a set of NormalizableScoringFunctions by a unified generative-discriminative learning principle
de.jstacs.classifier.scoringFunctionBased.logPrior	Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors
de.jstacs.classifier.scoringFunctionBased.msp	Provides an implementation of a classifier that allows to train the parameters of a set of ScoringFunctions either by maximum supervised posterior (MSP) or by maximum conditional likelihood (MCL)
de.jstacs.classifier.scoringFunctionBased.sampling	Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingScoringFunctions and that sample parameters using the Metropolis-Hastings algorithm.
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 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.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.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
de.jstacs.models.hmm.models	The package provides different implementations of hidden Markov models based on AbstractHMM
de.jstacs.models.hmm.states.emissions
de.jstacs.models.hmm.states.emissions.continuous
de.jstacs.models.hmm.states.emissions.discrete
de.jstacs.models.hmm.training	The package provides all classes used to determine the training algorithm of a hidden Markov model
de.jstacs.models.hmm.transitions	The package provides all interfaces and classes for transitions used in hidden Markov models.
de.jstacs.models.hmm.transitions.elements
de.jstacs.models.mixture	This package is the super package for any mixture model.
de.jstacs.models.mixture.motif
de.jstacs.models.mixture.motif.positionprior
de.jstacs.models.phylo
de.jstacs.models.phylo.parser
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.scoringFunctions	Provides ScoringFunctions that can be used in a ScoreClassifier.
de.jstacs.scoringFunctions.directedGraphicalModels	Provides ScoringFunctions 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 ScoringFunctions that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix	Provides ScoringFunctions that are mixtures of other ScoringFunctions.
de.jstacs.scoringFunctions.mix.motifSearch
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...
de.jstacs.utils.galaxy

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

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

AbsoluteValueCondition.AbsoluteValueConditionParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

AbsoluteValueCondition(StringBuffer xml)
Deprecated. The standard constructor for the interface Storable.

AbstractTerminationCondition.AbstractTerminationConditionParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

AbstractTerminationCondition(StringBuffer xml)
The standard constructor for the interface Storable.

CombinedCondition.CombinedConditionParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

CombinedCondition(StringBuffer xml)
The standard constructor for the interface Storable.

IterationCondition.IterationConditionParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

IterationCondition(StringBuffer xml)
The standard constructor for the interface Storable.

SmallDifferenceOfFunctionEvaluationsCondition.SmallDifferenceOfFunctionEvaluationsConditionParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

SmallDifferenceOfFunctionEvaluationsCondition(StringBuffer xml)
The standard constructor for the interface Storable.

SmallGradientConditon.SmallGradientConditonParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

SmallGradientConditon(StringBuffer xml)
The standard constructor for the interface Storable.

SmallStepCondition.SmallStepConditionParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

SmallStepCondition(StringBuffer xml)
The standard constructor for the interface Storable.

TimeCondition.TimeConditionParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

TimeCondition(StringBuffer xml)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.classifier

Methods in de.jstacs.classifier that throw NonParsableException

protected void	MappingClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
protected void	AbstractScoreBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
protected abstract void	AbstractClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml) Extracts further information of a classifier from an XML representation.
protected void	AbstractScoreBasedClassifier.DoubleTableResult.fromXML(StringBuffer representation)

Constructors in de.jstacs.classifier that throw NonParsableException

AbstractClassifier(StringBuffer xml)
The standard constructor for the interface Storable.

AbstractScoreBasedClassifier.DoubleTableResult(StringBuffer representation)
The standard constructor for the interface Storable .

AbstractScoreBasedClassifier(StringBuffer xml)
The standard constructor for the interface Storable.

ConfusionMatrix(StringBuffer representation)
The standard constructor for the interface Storable.

MappingClassifier(StringBuffer representation)
The standard constructor for the interface Storable.

MeasureParameters(StringBuffer representation)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.classifier.assessment

Constructors in de.jstacs.classifier.assessment that throw NonParsableException

ClassifierAssessmentAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

KFoldCVAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

RepeatedHoldOutAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

RepeatedSubSamplingAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

Sampled_RepeatedHoldOutAssessParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.classifier.modelBased

Methods in de.jstacs.classifier.modelBased that throw NonParsableException

protected void

ModelBasedClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)

Constructors in de.jstacs.classifier.modelBased that throw NonParsableException

ModelBasedClassifier(StringBuffer xml)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.classifier.scoringFunctionBased

Methods in de.jstacs.classifier.scoringFunctionBased that throw NonParsableException

protected void

ScoreClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)

Constructors in de.jstacs.classifier.scoringFunctionBased that throw NonParsableException

ScoreClassifier(StringBuffer xml)
The standard constructor for the interface Storable.

ScoreClassifierParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

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

Methods in de.jstacs.classifier.scoringFunctionBased.gendismix that throw NonParsableException

protected void

GenDisMixClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)

Constructors in de.jstacs.classifier.scoringFunctionBased.gendismix that throw NonParsableException

GenDisMixClassifier(StringBuffer xml)
This is the constructor for Storable.

GenDisMixClassifierParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

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

Constructors in de.jstacs.classifier.scoringFunctionBased.logPrior that throw NonParsableException

SeparateGaussianLogPrior(StringBuffer xml)
The standard constructor for the interface Storable.

SeparateLaplaceLogPrior(StringBuffer xml)
The standard constructor for the interface Storable.

SeparateLogPrior(StringBuffer xml)
The standard constructor for the interface Storable.

SimpleGaussianSumLogPrior(StringBuffer xml)
The standard constructor for the interface Storable.

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

Constructors in de.jstacs.classifier.scoringFunctionBased.msp that throw NonParsableException

MSPClassifier(StringBuffer xml)
This is the constructor for Storable.

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

Methods in de.jstacs.classifier.scoringFunctionBased.sampling that throw NonParsableException

protected void	SamplingScoreBasedClassifier.ScoringFunctionSamplingComponent.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.classifier.scoringFunctionBased.sampling that throw NonParsableException

SamplingGenDisMixClassifier(StringBuffer xml)
Creates a new SamplingGenDisMixClassifier from its XML-representation

SamplingScoreBasedClassifier(StringBuffer xml)
This is the constructor for Storable.

Uses of NonParsableException in de.jstacs.data

Methods in de.jstacs.data that throw NonParsableException

protected void	AlphabetContainerParameterSet.fromXML(StringBuffer representation)
void	AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet.fromXML(StringBuffer representation)
void	AlphabetContainerParameterSet.AlphabetArrayParameterSet.fromXML(StringBuffer representation)

Constructors in de.jstacs.data that throw NonParsableException

Alphabet.AlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable .

AlphabetContainer(StringBuffer xml)
The standard constructor for the interface Storable.

AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)
The standard constructor for the interface Storable .

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable .

AlphabetContainerParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.data.alphabets

Constructors in de.jstacs.data.alphabets that throw NonParsableException

ComplementableDiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface Storable.

ContinuousAlphabet.ContinuousAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable .

ContinuousAlphabet(StringBuffer xml)
The standard constructor for the interface Storable.

DiscreteAlphabet.DiscreteAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable .

DiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface Storable.

DiscreteAlphabetMapping(StringBuffer xml)
The standard constructor for the interface Storable.

DNAAlphabet.DNAAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable .

DNAAlphabet(StringBuffer representation)
The standard constructor for the interface Storable.

GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

GenericComplementableDiscreteAlphabet(StringBuffer representation)
The standard constructor for the interface Storable.

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

Methods in de.jstacs.data.sequences.annotation that throw NonParsableException

protected void	StrandedLocatedSequenceAnnotationWithLength.fromXML(StringBuffer representation)
protected void	SequenceAnnotation.fromXML(StringBuffer source)
protected void	LocatedSequenceAnnotationWithLength.fromXML(StringBuffer representation)
protected void	LocatedSequenceAnnotation.fromXML(StringBuffer representation)

Constructors in de.jstacs.data.sequences.annotation that throw NonParsableException

CisRegulatoryModuleAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

IntronAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

LocatedSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

LocatedSequenceAnnotationWithLength(StringBuffer representation)
The standard constructor for the interface Storable.

MotifAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

ReferenceSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

SequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

SinglePositionSequenceAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.io

Methods in de.jstacs.io that throw NonParsableException

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

Uses of NonParsableException in de.jstacs.models

Methods in de.jstacs.models that throw NonParsableException

protected void	VariableLengthWrapperModel.fromXML(StringBuffer xml)
void	UniformModel.fromXML(StringBuffer representation)
protected void	NormalizableScoringFunctionModel.fromXML(StringBuffer xml)
void	CompositeModel.fromXML(StringBuffer representation)
protected abstract void	AbstractModel.fromXML(StringBuffer xml) This method should only be used by the constructor that works on a StringBuffer.

Constructors in de.jstacs.models that throw NonParsableException

AbstractModel(StringBuffer stringBuff)
The standard constructor for the interface Storable.

CompositeModel(StringBuffer stringBuff)
The standard constructor for the interface Storable.

NormalizableScoringFunctionModel(StringBuffer stringBuff)
The standard constructor for the interface Storable.

UniformModel(StringBuffer stringBuff)
The standard constructor for the interface Storable.

VariableLengthWrapperModel(StringBuffer stringBuff)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.models.discrete

Methods in de.jstacs.models.discrete that throw NonParsableException

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

Constructors in de.jstacs.models.discrete that throw NonParsableException

Constraint(StringBuffer xml)
The standard constructor for the interface Storable.

DGMParameterSet(StringBuffer s)
The standard constructor for the interface Storable.

DiscreteGraphicalModel(DGMParameterSet params)
The default constructor.

DiscreteGraphicalModel(StringBuffer representation)
The standard constructor for the interface Storable.

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

Methods in de.jstacs.models.discrete.homogeneous that throw NonParsableException

protected void	HomogeneousModel.HomCondProb.extractAdditionalInfo(StringBuffer xml)
protected void	HomogeneousModel.set(DGMParameterSet params, boolean trained)
protected void	HomogeneousMM.set(DGMParameterSet params, boolean trained)
protected void	HomogeneousMM.setFurtherModelInfos(StringBuffer xml)

Constructors in de.jstacs.models.discrete.homogeneous that throw NonParsableException

HomogeneousMM(HomMMParameterSet params)
Creates a new homogeneous Markov model from a parameter set.

HomogeneousMM(StringBuffer stringBuff)
The standard constructor for the interface Storable.

HomogeneousModel.HomCondProb(StringBuffer xml)
The standard constructor for the interface Storable .

HomogeneousModel(HomogeneousModelParameterSet params)
Creates a homogeneous model from a parameter set.

HomogeneousModel(StringBuffer stringBuff)
The standard constructor for the interface Storable.

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

Constructors in de.jstacs.models.discrete.homogeneous.parameters that throw NonParsableException

HomMMParameterSet(StringBuffer s)
The standard constructor for the interface Storable.

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

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

Methods in de.jstacs.models.discrete.inhomogeneous that throw NonParsableException

protected void	MEMConstraint.extractAdditionalInfo(StringBuffer xml)
protected void	InhConstraint.extractAdditionalInfo(StringBuffer xml)
protected void	InhCondProb.extractAdditionalInfo(StringBuffer xml)
protected void	InhomogeneousDGM.set(DGMParameterSet parameter, boolean trained)
protected void	FSDAGModel.set(DGMParameterSet params, boolean trained)
protected void	BayesianNetworkModel.set(DGMParameterSet parameter, boolean trained)
protected void	FSDAGModelForGibbsSampling.setFurtherModelInfos(StringBuffer xml)
protected void	DAGModel.setFurtherModelInfos(StringBuffer xml)

Constructors in de.jstacs.models.discrete.inhomogeneous that throw NonParsableException

BayesianNetworkModel(BayesianNetworkModelParameterSet params)
Creates a new BayesianNetworkModel from a given BayesianNetworkModelParameterSet.

BayesianNetworkModel(StringBuffer representation)
The standard constructor for the interface Storable.

DAGModel(IDGMParameterSet params)
This is the main constructor.

DAGModel(StringBuffer xml)
The standard constructor for the interface Storable.

FSDAGModel(FSDAGMParameterSet params)
This is the main constructor.

FSDAGModel(StringBuffer xml)
The standard constructor for the interface Storable.

FSDAGModelForGibbsSampling(FSDAGModelForGibbsSamplingParameterSet params)
The default constructor.

FSDAGModelForGibbsSampling(StringBuffer representation)
This is the constructor for the Storable interface.

InhCondProb(StringBuffer xml)
The standard constructor for the interface Storable.

InhConstraint(StringBuffer xml)
The standard constructor for the interface Storable.

InhomogeneousDGM(IDGMParameterSet params)
Creates a new InhomogeneousDGM from a given IDGMParameterSet.

InhomogeneousDGM(StringBuffer representation)
The standard constructor for the interface Storable.

MEMConstraint(StringBuffer xml)
The standard constructor for the interface Storable.

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

Constructors in de.jstacs.models.discrete.inhomogeneous.parameters that throw NonParsableException

BayesianNetworkModelParameterSet(StringBuffer s)
The standard constructor for the interface Storable.

FSDAGModelForGibbsSamplingParameterSet(StringBuffer s)
The constructor for the Storable interface.

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

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

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

Methods in de.jstacs.models.discrete.inhomogeneous.shared that throw NonParsableException

protected void	SharedStructureClassifier.extractFurtherClassifierInfosFromXML(StringBuffer xml)
protected void	SharedStructureMixture.fromXML(StringBuffer representation)

Constructors in de.jstacs.models.discrete.inhomogeneous.shared that throw NonParsableException

SharedStructureClassifier(StringBuffer xml)
The standard constructor for the interface Storable.

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

Uses of NonParsableException in de.jstacs.models.hmm

Methods in de.jstacs.models.hmm that throw NonParsableException

protected abstract void	AbstractHMM.extractFurtherInformation(StringBuffer xml) This method extracts further information from the XML representation.
protected void	AbstractHMM.fromXML(StringBuffer xml) This method is used by the AbstractHMM.AbstractHMM(StringBuffer) constructor for creating an instance from an XML representation.

Constructors in de.jstacs.models.hmm that throw NonParsableException

AbstractHMM(StringBuffer xml)
The standard constructor for the interface Storable.

HMMTrainingParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.models.hmm.models

Methods in de.jstacs.models.hmm.models that throw NonParsableException

protected void	SamplingHigherOrderHMM.extractFurtherInformation(StringBuffer xml)
protected void	HigherOrderHMM.extractFurtherInformation(StringBuffer xml) This method extracts further information from the XML representation.
protected void	DifferentiableHigherOrderHMM.extractFurtherInformation(StringBuffer xml)

Constructors in de.jstacs.models.hmm.models that throw NonParsableException

DifferentiableHigherOrderHMM(StringBuffer xml)
The standard constructor for the interface Storable.

HigherOrderHMM(StringBuffer xml)
The standard constructor for the interface Storable.

SamplingHigherOrderHMM(StringBuffer xml)
The standard constructor for the interface Storable.

SamplingPhyloHMM(StringBuffer xml)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.models.hmm.states.emissions

Constructors in de.jstacs.models.hmm.states.emissions that throw NonParsableException

MixtureEmission(StringBuffer xml)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.models.hmm.states.emissions.continuous

Methods in de.jstacs.models.hmm.states.emissions.continuous that throw NonParsableException

protected void	PluginGaussianEmission.fromXML(StringBuffer xml)
protected void	GaussianEmission.fromXML(StringBuffer xml) This method is internally used by the constructor GaussianEmission.GaussianEmission(StringBuffer).

Constructors in de.jstacs.models.hmm.states.emissions.continuous that throw NonParsableException

GaussianEmission(StringBuffer xml)
Creates a GaussianEmission from its XML representation.

PluginGaussianEmission(StringBuffer xml)
Creates a PluginGaussianEmission from its XML representation.

Uses of NonParsableException in de.jstacs.models.hmm.states.emissions.discrete

Methods in de.jstacs.models.hmm.states.emissions.discrete that throw NonParsableException

protected void	ReferenceSequenceDiscreteEmission.extractFurtherInformation(StringBuffer xml)
protected void	PhyloDiscreteEmission.extractFurtherInformation(StringBuffer xml)
protected void	AbstractConditionalDiscreteEmission.extractFurtherInformation(StringBuffer xml) This method extracts further information from the XML representation.
protected void	AbstractConditionalDiscreteEmission.fromXML(StringBuffer xml) This method is internally used by the constructor AbstractConditionalDiscreteEmission.AbstractConditionalDiscreteEmission(StringBuffer).

Constructors in de.jstacs.models.hmm.states.emissions.discrete that throw NonParsableException

AbstractConditionalDiscreteEmission(StringBuffer xml)
Creates a AbstractConditionalDiscreteEmission from its XML representation.

DiscreteEmission(StringBuffer xml)
Creates a DiscreteEmission from its XML representation.

ReferenceSequenceDiscreteEmission(StringBuffer xml)
Creates a ReferenceSequenceDiscreteEmission from its XML representation.

Uses of NonParsableException in de.jstacs.models.hmm.training

Constructors in de.jstacs.models.hmm.training that throw NonParsableException

BaumWelchParameterSet(StringBuffer xml)
The standard constructor for the interface Storable.

MaxHMMTrainingParameterSet(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.models.hmm.transitions

Methods in de.jstacs.models.hmm.transitions that throw NonParsableException

protected void	HigherOrderTransition.extractFurtherInformation(StringBuffer xml)
protected void	BasicHigherOrderTransition.extractFurtherInformation(StringBuffer xml) This method extracts further information from the XML representation.
protected abstract void	BasicHigherOrderTransition.AbstractTransitionElement.extractFurtherInformation(StringBuffer xml) This method extracts further information from the XML representation.

Constructors in de.jstacs.models.hmm.transitions that throw NonParsableException

BasicHigherOrderTransition.AbstractTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable.

BasicHigherOrderTransition(StringBuffer xml)
The standard constructor for the interface Storable.

HigherOrderTransition(StringBuffer xml)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.models.hmm.transitions.elements

Methods in de.jstacs.models.hmm.transitions.elements that throw NonParsableException

protected void	ScaledTransitionElement.extractFurtherInformation(StringBuffer xml)
protected void	ReferenceBasedTransitionElement.extractFurtherInformation(StringBuffer xml)
protected void	DistanceBasedScaledTransitionElement.extractFurtherInformation(StringBuffer xml)
protected void	BasicTransitionElement.extractFurtherInformation(StringBuffer xml)
protected void	BasicPluginTransitionElement.extractFurtherInformation(StringBuffer xml)

Constructors in de.jstacs.models.hmm.transitions.elements that throw NonParsableException

BasicPluginTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable.

BasicTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable.

DistanceBasedScaledTransitionElement(StringBuffer xml)
Extracts a distance-base scaled transition element from XML.

ReferenceBasedTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable.

ScaledTransitionElement(StringBuffer xml)
The standard constructor for the interface Storable.

TransitionElement(StringBuffer xml)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.models.mixture

Methods in de.jstacs.models.mixture that throw NonParsableException

protected void	AbstractMixtureModel.extractFurtherInformation(StringBuffer xml) This method is used in the subclasses to extract further information from the XML representation and to set these as values of the instance.
protected void	AbstractMixtureModel.fromXML(StringBuffer representation)

Constructors in de.jstacs.models.mixture that throw NonParsableException

AbstractMixtureModel(StringBuffer xml)
The standard constructor for the interface Storable.

MixtureModel(StringBuffer xml)
The constructor for the interface Storable.

StrandModel(StringBuffer stringBuff)
The constructor for the interface Storable.

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

Methods in de.jstacs.models.mixture.motif that throw NonParsableException

protected void

HiddenMotifMixture.extractFurtherInformation(StringBuffer xml)

Constructors in de.jstacs.models.mixture.motif that throw NonParsableException

HiddenMotifMixture(StringBuffer xml)
The standard constructor for the interface Storable.

SingleHiddenMotifMixture(StringBuffer xml)
The standard constructor for the interface Storable.

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

Methods in de.jstacs.models.mixture.motif.positionprior that throw NonParsableException

protected abstract void	PositionPrior.extractAdditionalInformation(StringBuffer xml) This method extracts additional information from a StringBuffer.
protected void	GaussianLikePositionPrior.extractAdditionalInformation(StringBuffer xml)

Constructors in de.jstacs.models.mixture.motif.positionprior that throw NonParsableException

GaussianLikePositionPrior(StringBuffer rep)
The standard constructor for the interface Storable.

PositionPrior(StringBuffer rep)
The standard constructor for the interface Storable.

UniformPositionPrior(StringBuffer xml)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.models.phylo

Constructors in de.jstacs.models.phylo that throw NonParsableException

PhyloNode(StringBuffer xml)
The standard constructor for the interface Storable.

PhyloTree(StringBuffer xml)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.models.phylo.parser

Methods in de.jstacs.models.phylo.parser that throw NonParsableException

PhyloTree

NewickParser.tokenize() This method construct a PhyloTree from the given input stream

Uses of NonParsableException in de.jstacs.motifDiscovery.history

Constructors in de.jstacs.motifDiscovery.history that throw NonParsableException

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

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

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

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

Uses of NonParsableException in de.jstacs.parameters

Methods in de.jstacs.parameters that throw NonParsableException

protected void	EnumParameter.extractCollection(StringBuffer buf)
protected void	CollectionParameter.extractCollection(StringBuffer buf) Extracts the internal ParameterSet from its XML representation ( ParameterSet.toXML()).
protected void	SimpleParameter.fromXML(StringBuffer representation)
protected void	SequenceScoringParameterSet.fromXML(StringBuffer representation)
protected void	RangeParameter.fromXML(StringBuffer representation)
protected void	ParameterSetContainer.fromXML(StringBuffer representation)
protected void	ParameterSet.fromXML(StringBuffer representation) Parses the instance fields of a ParameterSet from the XML representation as returned by ParameterSet.toXML().
protected void	Parameter.fromXML(StringBuffer source) Parses a Parameter from a XML representation as returned by Parameter.toXML().
protected void	MultiSelectionCollectionParameter.fromXML(StringBuffer representation)
protected void	InstanceParameterSet.fromXML(StringBuffer representation)
protected void	FileParameter.fromXML(StringBuffer representation)
protected void	ExpandableParameterSet.fromXML(StringBuffer representation)
protected void	CollectionParameter.fromXML(StringBuffer representation)
protected void	ArrayParameterSet.fromXML(StringBuffer representation)

Constructors in de.jstacs.parameters that throw NonParsableException

ArrayParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

CollectionParameter(StringBuffer representation)
The standard constructor for the interface Storable.

EnumParameter(StringBuffer representation)
The standard constructor for the interface Storable.

ExpandableParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

FileParameter.FileRepresentation(StringBuffer buf)
The standard constructor for the interface Storable .

FileParameter(StringBuffer buf)
The standard constructor for the interface Storable.

InstanceParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

MultiSelectionCollectionParameter(StringBuffer representation)
The standard constructor for the interface Storable.

ParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

ParameterSetContainer(StringBuffer representation)
The standard constructor for the interface Storable.

RangeParameter(StringBuffer representation)
The standard constructor for the interface Storable.

SequenceScoringParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

SimpleParameter(StringBuffer representation)
The standard constructor for the interface Storable.

SimpleParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.parameters.validation

Methods in de.jstacs.parameters.validation that throw NonParsableException

void	StorableValidator.fromXML(StringBuffer representation) Parses a StorableValidator from the XML representation as returned by StorableValidator.toXML().
void	SimpleStaticConstraint.fromXML(StringBuffer representation) Parses a SimpleStaticConstraint from the XML representation as returned by SimpleStaticConstraint.toXML().
void	SimpleReferenceConstraint.fromXML(StringBuffer representation)
void	ReferenceConstraint.fromXML(StringBuffer representation) Parses a ReferenceConstraint from the XML representation as returned by ReferenceConstraint.toXML().
void	NumberValidator.fromXML(StringBuffer representation) Parses a NumberValidator from the XML representation as returned by NumberValidator.toXML().
void	ConstraintValidator.fromXML(StringBuffer representation) Parses a ConstraintValidator from the XML representation as returned by ConstraintValidator.toXML().

Constructors in de.jstacs.parameters.validation that throw NonParsableException

ConstraintValidator(StringBuffer representation)
The standard constructor for the interface Storable.

NumberValidator(StringBuffer representation)
The standard constructor for the interface Storable.

ReferenceConstraint(StringBuffer representation)
The standard constructor for the interface Storable.

SimpleReferenceConstraint(StringBuffer representation)
The standard constructor for the interface Storable.

SimpleStaticConstraint(StringBuffer representation)
The standard constructor for the interface Storable.

StorableValidator(StringBuffer buf)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.results

Methods in de.jstacs.results that throw NonParsableException

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

Constructors in de.jstacs.results that throw NonParsableException

CategoricalResult(StringBuffer representation)
The standard constructor for the interface Storable.

ImageResult(StringBuffer xml)
The standard constructor for the interface Storable.

ListResult(StringBuffer representation)
The standard constructor for the interface Storable.

MeanResultSet(StringBuffer representation)
The standard constructor for the interface Storable.

NumericalResult(StringBuffer representation)
The standard constructor for the interface Storable.

NumericalResultSet(StringBuffer representation)
The standard constructor for the interface Storable.

Result(StringBuffer rep)
The standard constructor for the interface Storable.

ResultSet(StringBuffer representation)
The standard constructor for the interface Storable.

SampleResult(StringBuffer source)
The standard constructor for the interface Storable.

SimpleResult(StringBuffer rep)
This is the constructor for Storable.

StorableResult(StringBuffer buf)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.sampling

Methods in de.jstacs.sampling that throw NonParsableException

protected void	VarianceRatioBurnInTest.setFurtherInformation(StringBuffer xml)
protected abstract void	AbstractBurnInTest.setFurtherInformation(StringBuffer xml) This method sets further information for the AbstractBurnInTest.

Constructors in de.jstacs.sampling that throw NonParsableException

AbstractBurnInTest(StringBuffer rep)
This is the constructor for the Storable interface.

AbstractBurnInTestParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

SimpleBurnInTest(StringBuffer xml)
Deprecated. The standard constructor for the interface Storable.

VarianceRatioBurnInTest(StringBuffer rep)
The standard constructor for the Storable interface.

VarianceRatioBurnInTestParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.scoringFunctions

Methods in de.jstacs.scoringFunctions that throw NonParsableException

protected void	UniformScoringFunction.fromXML(StringBuffer xml)
protected void	NormalizedScoringFunction.fromXML(StringBuffer xml)
protected void	MRFScoringFunction.fromXML(StringBuffer representation)
protected void	MappingScoringFunction.fromXML(StringBuffer xml)
protected void	IndependentProductScoringFunction.fromXML(StringBuffer rep)
protected void	CMMScoringFunction.fromXML(StringBuffer xml)
protected abstract void	AbstractNormalizableScoringFunction.fromXML(StringBuffer xml) This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.

Constructors in de.jstacs.scoringFunctions that throw NonParsableException

AbstractNormalizableScoringFunction(StringBuffer xml)
This is the constructor for Storable.

AbstractVariableLengthScoringFunction(StringBuffer source)
This is the constructor for the interface Storable.

CMMScoringFunction(StringBuffer source)
This is the constructor for Storable.

IndependentProductScoringFunction(StringBuffer source)
This is the constructor for the interface Storable.

MappingScoringFunction(StringBuffer xml)
This is the constructor for Storable.

MRFScoringFunction(StringBuffer source)
This is the constructor for the interface Storable.

NormalizedScoringFunction(StringBuffer xml)
This is the constructor for Storable.

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

Uses of NonParsableException in de.jstacs.scoringFunctions.directedGraphicalModels

Methods in de.jstacs.scoringFunctions.directedGraphicalModels that throw NonParsableException

protected void	MutableMarkovModelScoringFunction.fromXML(StringBuffer source)
protected void	BayesianNetworkScoringFunction.fromXML(StringBuffer source)

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels that throw NonParsableException

BayesianNetworkScoringFunction(StringBuffer xml)
The standard constructor for the interface Storable.

BayesianNetworkScoringFunctionParameterSet(StringBuffer representation)
Creates a new BayesianNetworkScoringFunctionParameterSet from its XML representation as defined by the Storable interface.

MutableMarkovModelScoringFunction(StringBuffer xml)
The standard constructor for the interface Storable.

Parameter(StringBuffer representation)
The standard constructor for the interface Storable.

ParameterTree.TreeElement(StringBuffer representation)
Constructor for the Storable interface.

ParameterTree(StringBuffer source)
Recreates a ParameterTree from its XML representation as returned by ParameterTree.toXML().

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

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures that throw NonParsableException

InhomogeneousMarkov.InhomogeneousMarkovParameterSet(StringBuffer representation)
Creates a new InhomogeneousMarkov.InhomogeneousMarkovParameterSet from its XML representation as defined by the Storable interface.

InhomogeneousMarkov(StringBuffer buf)
The standard constructor for the interface Storable.

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

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures that throw NonParsableException

BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet(StringBuffer representation)
The standard constructor for the interface Storable .

BTExplainingAwayResidual(StringBuffer buf)
The standard constructor for the interface Storable.

BTMutualInformation.BTMutualInformationParameterSet(StringBuffer representation)
The standard constructor for the interface Storable .

BTMutualInformation(StringBuffer buf)
The standard constructor for the interface Storable.

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

Constructors in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.pmmMeasures that throw NonParsableException

PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet(StringBuffer representation)
Creates a new PMMExplainingAwayResidual.PMMExplainingAwayResidualParameterSet from its XML representation as defined by the Storable interface.

PMMExplainingAwayResidual(StringBuffer buf)
The standard constructor for the interface Storable.

PMMMutualInformation.PMMMutualInformationParameterSet(StringBuffer representation)
Creates a new PMMMutualInformation.PMMMutualInformationParameterSet from its XML representation as defined by the Storable interface.

PMMMutualInformation(StringBuffer buf)
The standard constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.scoringFunctions.homogeneous

Methods in de.jstacs.scoringFunctions.homogeneous that throw NonParsableException

protected void	UniformHomogeneousScoringFunction.fromXML(StringBuffer xml)
protected void	HMMScoringFunction.fromXML(StringBuffer xml)
protected void	HMM0ScoringFunction.fromXML(StringBuffer xml)

Constructors in de.jstacs.scoringFunctions.homogeneous that throw NonParsableException

HMM0ScoringFunction(StringBuffer xml)
This is the constructor for Storable.

HMMScoringFunction(StringBuffer xml)
This is the constructor for Storable.

HomogeneousScoringFunction(StringBuffer source)
This is the constructor for Storable.

UniformHomogeneousScoringFunction(StringBuffer xml)
This is the constructor for Storable.

Uses of NonParsableException in de.jstacs.scoringFunctions.mix

Methods in de.jstacs.scoringFunctions.mix that throw NonParsableException

protected void	StrandScoringFunction.extractFurtherInformation(StringBuffer xml)
protected void	AbstractMixtureScoringFunction.extractFurtherInformation(StringBuffer xml) This method is the opposite of AbstractMixtureScoringFunction.getFurtherInformation().
protected void	AbstractMixtureScoringFunction.fromXML(StringBuffer b)

Constructors in de.jstacs.scoringFunctions.mix that throw NonParsableException

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

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

StrandScoringFunction(StringBuffer xml)
This is the constructor for Storable.

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

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

Methods in de.jstacs.scoringFunctions.mix.motifSearch that throw NonParsableException

protected void	HiddenMotifsMixture.extractFurtherInformation(StringBuffer xml)
protected void	SkewNormalLikeScoringFunction.fromXML(StringBuffer rep)
protected void	PositionScoringFunction.fromXML(StringBuffer xml)
protected void	MixtureDuration.fromXML(StringBuffer rep)
protected void	DurationScoringFunction.fromXML(StringBuffer xml)

Constructors in de.jstacs.scoringFunctions.mix.motifSearch that throw NonParsableException

DurationScoringFunction(StringBuffer source)
This is the constructor for Storable.

HiddenMotifsMixture(StringBuffer source)
This is the constructor for the interface Storable.

MixtureDuration(StringBuffer source)
This is the constructor for Storable.

PositionScoringFunction(StringBuffer source)
This is the constructor for Storable.

SkewNormalLikeScoringFunction(StringBuffer source)
This is the constructor for Storable.

UniformDurationScoringFunction(StringBuffer b)
This is the constructor for Storable.

Uses of NonParsableException in de.jstacs.utils

Constructors in de.jstacs.utils that throw NonParsableException

DoubleList(StringBuffer rep)
This is the constructor for the interface Storable.

Uses of NonParsableException in de.jstacs.utils.galaxy

Methods in de.jstacs.utils.galaxy that throw NonParsableException

protected void	GalaxyAdaptor.LinkedImageResult.fromXML(StringBuffer representation)
protected void	GalaxyAdaptor.FileResult.fromXML(StringBuffer rep)

Constructors in de.jstacs.utils.galaxy that throw NonParsableException

GalaxyAdaptor.FileResult(StringBuffer rep)
Creates a new GalaxyAdaptor.FileResult from its XML-representation

GalaxyAdaptor.LinkedImageResult(StringBuffer xml)
Creates a new GalaxyAdaptor.LinkedImageResult from its XML-representation