Uses of Class
de.jstacs.NonParsableException

Packages that use NonParsableException
de.jstacs.classifier This package provides the framework for any classifier. 
de.jstacs.classifier.assessment This package allows to assess classifiers. 
de.jstacs.classifier.modelBased Provides the classes for Classifiers that are based on Model
de.jstacs.classifier.scoringFunctionBased Provides the classes for Classifiers that are based on ScoringFunctions. 
de.jstacs.classifier.scoringFunctionBased.cll Provides the implementation of the log conditional likelihood as an OptimizableFunction and a classifier that uses log conditional likelihood or supervised posterior to learn the parameters of a set of ScoringFunctions 
de.jstacs.classifier.scoringFunctionBased.logPrior Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors 
de.jstacs.data Provides classes for the representation of data. 
de.jstacs.data.alphabets Provides classes for the representation of discrete and continuous alphabets, including a DNAAlphabet for the most common case of DNA-sequences 
de.jstacs.data.sequences.annotation Provides the facilities to annotate 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.mixture This package is the super package for any mixture model. 
de.jstacs.models.mixture.gibbssampling This package contains many classes that can be used while a Gibbs sampling. 
de.jstacs.models.mixture.motif   
de.jstacs.models.mixture.motif.positionprior   
de.jstacs.parameters This package provides classes for parameters that establish a general convention for the description of parameters as defined in the Parameter-interface. 
de.jstacs.parameters.validation Provides classes for the validation of Parameter values 
de.jstacs.results This package provides classes for results and sets of results. 
de.jstacs.scoringFunctions Provides 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 ... 
 

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.cll
 

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

Constructors in de.jstacs.classifier.scoringFunctionBased.cll that throw NonParsableException
CLLClassifier(StringBuffer xml)
          The standard constructor for the interface Storable.
CLLClassifierParameterSet(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.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.
DNAAlphabet.DNAAlphabetParameterSet(StringBuffer representation)
          The standard constructor for the interface Storable .
DNAAlphabet(StringBuffer representation)
          The standard constructor for the interface Storable.
 

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

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

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

Uses of NonParsableException in de.jstacs.models
 

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

Uses of NonParsableException in de.jstacs.models.discrete
 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Uses of NonParsableException in de.jstacs.models.mixture
 

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

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

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

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

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

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

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

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

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

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

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

Uses of NonParsableException in de.jstacs.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.
ListResult(StringBuffer representation)
          The standard constructor for the interface Storable.
MeanResultSet(StringBuffer representation)
          The standard constructor for the interface Storable.
NumericalResult(StringBuffer representation)
          The standard constructor for the interface Storable.
NumericalResultSet(StringBuffer representation)
          The standard constructor for the interface Storable.
Result(StringBuffer rep)
          The standard constructor for the interface Storable.
ResultSet(StringBuffer representation)
          The standard constructor for the interface Storable.
SampleResult(StringBuffer source)
          The standard constructor for the interface Storable.
SimpleResult(StringBuffer rep)
          This is the constructor for Storable.
StorableResult(StringBuffer buf)
          The standard constructor for the interface Storable.
 

Uses of NonParsableException in de.jstacs.scoringFunctions
 

Methods in de.jstacs.scoringFunctions that throw NonParsableException
protected  void UniformScoringFunction.fromXML(StringBuffer xml)
           
protected  void NormalizedScoringFunction.fromXML(StringBuffer xml)
           
protected  void MRFScoringFunction.fromXML(StringBuffer representation)
           
protected  void IndependentProductScoringFunction.fromXML(StringBuffer rep)
           
protected 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.
IndependentProductScoringFunction(StringBuffer source)
          This is the constructor for the interface Storable.
MRFScoringFunction(StringBuffer source)
          This is the constructor for the interface Storable.
NormalizedScoringFunction(StringBuffer xml)
          This is the constructor for Storable.
UniformScoringFunction(StringBuffer xml)
          This is the constructor for the interface Storable.
VariableLengthScoringFunction(StringBuffer source)
          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
static ParameterTree[] ParameterTree.fromStringArray(String[] strs, AlphabetContainer alphabet)
          Recreates an array of ParameterTrees from their XML representation as given in strs.
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(StringBuffer source, AlphabetContainer alphabet)
          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.
 

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 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.
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.