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A B C D E F G H I K L M N O P Q R S T U V W X

## A

AbstractBurnInTest - Class in de.jstacs.models.mixture.gibbssampling
  This abstract class implements some of the methods of `BurnInTest` to alleviate the implementation of efficient and new burn-in tests.
AbstractBurnInTest(int) - Constructor for class de.jstacs.models.mixture.gibbssampling.AbstractBurnInTest
  This is the main constructor that creates a burn-in test for a specified number of Gibbs sampling starts.
AbstractBurnInTest(StringBuffer) - Constructor for class de.jstacs.models.mixture.gibbssampling.AbstractBurnInTest
  This is the constructor for the interface `Storable`.
AbstractClassifier - Class in de.jstacs.classifier
  The super class for any classifier.
AbstractClassifier(AlphabetContainer) - Constructor for class de.jstacs.classifier.AbstractClassifier
  The constructor for a homogeneous classifier.
AbstractClassifier(AlphabetContainer, int) - Constructor for class de.jstacs.classifier.AbstractClassifier
  The constructor for an inhomogeneous classifier.
AbstractClassifier(StringBuffer) - Constructor for class de.jstacs.classifier.AbstractClassifier
  The constructor for the `Storable` interface.
AbstractMixtureModel - Class in de.jstacs.models.mixture
  This is the abstract class for all kinds of mixture models.
AbstractMixtureModel(int, Model[], boolean[], int, int, boolean, double[], double[], AbstractMixtureModel.Algorithm, double, double, AbstractMixtureModel.Parameterization, int, int, BurnInTest) - Constructor for class de.jstacs.models.mixture.AbstractMixtureModel
  Creates a new AbstractMixtureModel.
AbstractMixtureModel(StringBuffer) - Constructor for class de.jstacs.models.mixture.AbstractMixtureModel
  The standard constructor for the interface `Storable`.
AbstractMixtureModel.Algorithm - Enum in de.jstacs.models.mixture
  This enum defines the different types of algorithms that can be used in a `AbstractMixtureModel`
AbstractMixtureModel.Parameterization - Enum in de.jstacs.models.mixture
  This enum defines the different types of parameterization for a probability that can be used in an `AbstractMixtureModel`.
AbstractMixtureScoringFunction - Class in de.jstacs.scoringFunctions.mix
  This main abstract class for any mixture (e.g.
AbstractMixtureScoringFunction(int, int, int, boolean, boolean, NormalizableScoringFunction...) - Constructor for class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
  This constructor creates an AbstractMixtureScoringFunction.
AbstractMixtureScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
  This is the constructor for `Storable`.
AbstractModel - Class in de.jstacs.models
  Abstract class for a model for pattern recognition.
AbstractModel(AlphabetContainer, int) - Constructor for class de.jstacs.models.AbstractModel
  Constructor that sets the length of the model to `length` and the AlphabetContainer to `alphabets`.
AbstractModel(StringBuffer) - Constructor for class de.jstacs.models.AbstractModel
  Constructor for parsing a AbstractModel out of a StringBuffer.
AbstractNormalizableScoringFunction - Class in de.jstacs.scoringFunctions
  This class is the main part of any ScoreClassifier.
AbstractNormalizableScoringFunction(AlphabetContainer, int) - Constructor for class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
  The main constructor.
AbstractNormalizableScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
  This is the constructor for `Storable`.
AbstractOptimizableFunction - Class in de.jstacs.classifier.scoringFunctionBased
  This class extends `OptimizableFunction` and implements some common methods.
AbstractOptimizableFunction(Sample[], double[][], boolean, boolean) - Constructor for class de.jstacs.classifier.scoringFunctionBased.AbstractOptimizableFunction
  The constructor creates an instance using the given weighted data.
AbstractScoreBasedClassifier - Class in de.jstacs.classifier
  This class is the main class for all score based classifiers.
AbstractScoreBasedClassifier(AlphabetContainer, int) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The constructor for a homogeneous classifier.
AbstractScoreBasedClassifier(AlphabetContainer, int, double) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The constructor for a homogeneous classifier.
AbstractScoreBasedClassifier(AlphabetContainer, int, int) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The constructor for an inhomogeneous classifier.
AbstractScoreBasedClassifier(AlphabetContainer, int, int, double) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The constructor for an inhomogeneous classifier.
AbstractScoreBasedClassifier(StringBuffer) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier
  The constructor for the `Storable` interface.
AbstractScoreBasedClassifier.DoubleTableResult - Class in de.jstacs.classifier
  This class is for a table of `double`s.
AbstractScoreBasedClassifier.DoubleTableResult(StringBuffer) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier.DoubleTableResult
  This is the constructor for the interface `Storable`.
AbstractStringExtractor - Class in de.jstacs.io
  This class implements the reader that extracts strings.
AbstractStringExtractor(char) - Constructor for class de.jstacs.io.AbstractStringExtractor
  This constructor creates an instance with the specified character as start of each comment line.
accept(File) - Method in class de.jstacs.io.SubstringFilenameFilter
accept(File, String) - Method in class de.jstacs.io.SubstringFilenameFilter
actionPerformed(ActionEvent) - Method in class de.jstacs.utils.GUIProgressUpdater
add(int, int) - Method in class de.jstacs.classifier.ConfusionMatrix
  This method updates the confusion matrix.
add(int, double) - Method in class de.jstacs.models.discrete.Constraint
  Adds the `weight` to the count with index `index`.
add(Sequence, int, double) - Method in class de.jstacs.models.discrete.Constraint
  This method determines the specific constraint that is fulfilled by the sequence and adds the `weight` to the specific counter.
add(int, Parameter) - Method in class de.jstacs.parameters.ParameterSet.ParameterList
add(Parameter) - Method in class de.jstacs.parameters.ParameterSet.ParameterList
add(double) - Method in class de.jstacs.utils.DoubleList
  Adds the element `val` at the end of the list.
add(double, int, int) - Method in class de.jstacs.utils.DoubleList
  Adds the element `val` from `fromIndex` to `toIndex` (exclusive).
add(int) - Method in class de.jstacs.utils.IntList
  Adds the element `val` at the end of the list.
addAll(Collection<? extends Parameter>) - Method in class de.jstacs.parameters.ParameterSet.ParameterList
addAll(int, Collection<? extends Parameter>) - Method in class de.jstacs.parameters.ParameterSet.ParameterList
addConstraint(Constraint) - Method in class de.jstacs.parameters.validation.ConstraintValidator
  Adds an additional `Constraint` to the list of `Constraint`s.
addCount(double) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.Parameter
  Adds `count2` the the counts of this parameter.
addCount(Sequence, int, double) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree
  Adds `count` to the parameter as returned by `ParameterTree.getParameterFor(Sequence, int)`.
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.DoesNothingLogPrior
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.LogPrior
  Adds the gradient of the log-prior using the current parameters to a given vector.
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateGaussianLogPrior
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLaplaceLogPrior
addGradientFor(double[], double[]) - Method in class de.jstacs.classifier.scoringFunctionBased.logPrior.SimpleGaussianSumLogPrior
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.homogeneous.HMM0ScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.homogeneous.HMMScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.homogeneous.UniformHomogeneousScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.IndependentProductScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.MRFScoringFunction
addGradientOfLogPriorTerm(double[], int) - Method in interface de.jstacs.scoringFunctions.NormalizableScoringFunction
  This method computes the gradient of `getLogPriorTerm()` for each parameter of this model.
addGradientOfLogPriorTerm(double[], int) - Method in class de.jstacs.scoringFunctions.UniformScoringFunction
addParameterToSet() - Method in class de.jstacs.parameters.ExpandableParameterSet
  Adds a new `ParameterSetContainer` containing a clone of the `ParameterSet`-template to the set of `Parameter`s
addResults(MeanResultSet, MeanResultSet) - Static method in class de.jstacs.results.MeanResultSet
  Adds two `MeanResultsSet`s.
addResults(NumericalResultSet...) - Method in class de.jstacs.results.MeanResultSet
  Adds NumericalResultSets to this MenResultSet.
addTags(StringBuffer, String) - Static method in class de.jstacs.io.XMLParser
  Frames the StringBuffer `source` with "< `tag` >" and "< `/tag` >"
addTags(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Frames the StringBuffer `source` with "< `startTag` >" and "< `/endTag` >"
addTermToClassParameter(int, double) - Method in class de.jstacs.classifier.scoringFunctionBased.AbstractOptimizableFunction
addTermToClassParameter(int, double) - Method in class de.jstacs.classifier.scoringFunctionBased.OptimizableFunction
  This method adds the `term` to the class parameter.
algorithm - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
  The type of algorithm.
algorithmHasBeenRun - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
  A switch which indicates that the algorithm has been run for determining the parameters.
algorithmHasBeenRun() - Method in class de.jstacs.models.mixture.AbstractMixtureModel
  This method indicates whether the parameters of the model has been determined by the internal algorithm.
Alignment - Class in de.jstacs.algorithms
  Class for gapped global alignments using the extended Needleman-Wunsch algorithm.
Alignment(Sequence, Sequence, Alignment.Costs) - Constructor for class de.jstacs.algorithms.Alignment
  Creates a new `Alignment.StringAlignment` instance that aligns the sequences `s1` and `s2` using the costs defined in `costs`.
Alignment.Costs - Interface in de.jstacs.algorithms
  General interface for the costs of an alignment.
Alignment.Costs.Direction - Enum in de.jstacs.algorithms
  The direction of the predecessor in the DP-matrix
Alignment.SimpleCosts - Class in de.jstacs.algorithms
  Class for simple costs with costs `mismatch` for a mismatch, costs `start` to start a new gap, `elong` to elongate a gap by one position, and costs of `0` for a match
Alignment.SimpleCosts(double, double, double) - Constructor for class de.jstacs.algorithms.Alignment.SimpleCosts
  Creates a new instance of simple costs with costs `mismatch` for a mismatch, costs `start` to start a new gap, `elong` to elongate a gap by one position, and costs of `0` for a match
Alignment.StringAlignment - Class in de.jstacs.algorithms
  Class for the representation of an alignment of two strings.
Alignment.StringAlignment(String, String, double) - Constructor for class de.jstacs.algorithms.Alignment.StringAlignment
  Creates the instance for the two (extended) strings and the edit-costs.
Alphabet - Class in de.jstacs.data
  Class for an `Alphabet`.
Alphabet() - Constructor for class de.jstacs.data.Alphabet
alphabet - Variable in class de.jstacs.parameters.SequenceScoringParameterSet
  The alphabet the model works on
Alphabet.AlphabetParameterSet - Class in de.jstacs.data
  The super class for the `InstanceParameterSet` of any `Alphabet`.
Alphabet.AlphabetParameterSet(Class<? extends Alphabet>) - Constructor for class de.jstacs.data.Alphabet.AlphabetParameterSet
  Creates a new `Alphabet.AlphabetParameterSet`.
Alphabet.AlphabetParameterSet(StringBuffer) - Constructor for class de.jstacs.data.Alphabet.AlphabetParameterSet
  Creates a new `Alphabet.AlphabetParameterSet` from its XML representation.
alphabetCon - Variable in class de.jstacs.data.Sequence
  the underlying alphabets
AlphabetContainer - Class in de.jstacs.data
  The container for some alphabets used in a sequence, sample, model or ... .
AlphabetContainer(Alphabet) - Constructor for class de.jstacs.data.AlphabetContainer
  This constructor creates a simple `AlphabetContainer`.
AlphabetContainer(Alphabet[]) - Constructor for class de.jstacs.data.AlphabetContainer
  This constructor creates an `AlphabetContainer` with different alphabets for each position.
AlphabetContainer(AlphabetContainer[], int[]) - Constructor for class de.jstacs.data.AlphabetContainer
  This constructor creates an new sparse `AlphabetContainer` based on given `AlphabetContainer`s.
AlphabetContainer(Alphabet[], int[]) - Constructor for class de.jstacs.data.AlphabetContainer
  This constructor creates an `AlphabetContainer` that uses different alphabets.
AlphabetContainer(AlphabetContainerParameterSet) - Constructor for class de.jstacs.data.AlphabetContainer
  Creates a new `AlphabetContainer` from an `AlphabetContainerParameterSet` that contains all necessary parameters.
AlphabetContainer(StringBuffer) - Constructor for class de.jstacs.data.AlphabetContainer
  Extracts the `AlphabetContainerParameterSet` from a `StringBuffer`.
AlphabetContainer.AlphabetContainerType - Enum in de.jstacs.data
  Possible types of `AlphabetContainer`s are discrete alphabets, continuous alphabets, or alphabets mixed of discrete and continuous symbols at different positions.
AlphabetContainerParameterSet - Class in de.jstacs.data
  Class for the `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` of an `AlphabetContainer`.
AlphabetContainerParameterSet(AlphabetContainer.AlphabetContainerType, boolean) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  Creates a new `AlphabetContainerParameterSet`.
AlphabetContainerParameterSet(StringBuffer) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  Creates a new `AlphabetContainerParameterSet` from its XML representation.
AlphabetContainerParameterSet(Alphabet) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  Creates a new `AlphabetContainerParameterSet` from a single `Alphabet`.
AlphabetContainerParameterSet(Alphabet[]) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  Creates a new `AlphabetContainerParameterSet` from an array of `Alphabet`s.
AlphabetContainerParameterSet(Alphabet[], int[]) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
  Creates a new `AlphabetContainerParameterSet` from an array of `Alphabet`s and an array of `int`s defining the number of the alphabet in `alphabets` that is used for that position in `indexes`.
AlphabetContainerParameterSet.AlphabetArrayParameterSet - Class in de.jstacs.data
  Class for the parameters of an array of `Alphabet`s of defined length.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
  Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from the information if the array shall contain only the parameters for discrete `Alphabet`s.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
  Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from its XML representation.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[], AlphabetContainer.AlphabetContainerType) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
  Creates a new `AlphabetContainerParameterSet.AlphabetArrayParameterSet` from an array of `Alphabet`s and the information if all alphabets are discrete.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet - Class in de.jstacs.data
  Class for the parameters of an array of `Alphabet`s where each alphabet may be used for one or more sections of positions.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(AlphabetContainer.AlphabetContainerType) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
  Creates a new `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` for a set of discrete or continuous alphabets.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[], int[]) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
  Creates a new `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` from an array of `Alphabet`s, an array of indexes that define the index of the `Alphabet` in `alphabets` belonging to that position in `indexes` and a parameter if the alphabets may be discrete only.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
  Creates a new `AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet` from its XML representation.
alphabets - Variable in class de.jstacs.models.AbstractModel
  The underlying alphabets
alphabets - Variable in class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
  The AlphabetContainer of this `NormalizableScoringFunction`
alternativeModel - Variable in class de.jstacs.models.mixture.AbstractMixtureModel
  The alternative models for the EM.
annotate(boolean, SequenceAnnotation...) - Method in class de.jstacs.data.Sequence
  This method allows to append annotation to a sequence.
annotation - Variable in class de.jstacs.data.Sequence
  The annotation of the sequence.
annotation - Variable in class de.jstacs.io.AbstractStringExtractor
  The annotation of the source.
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.Constraint
  This method appends additional information that are not stored in the base class to the StringBuffer.
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.homogeneous.HomogeneousModel.HomCondProb
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.InhCondProb
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.InhConstraint
appendAdditionalInfo(StringBuffer) - Method in class de.jstacs.models.discrete.inhomogeneous.MEMConstraint
appendBoolean2ArrayWithTags(StringBuffer, boolean[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional boolean array with equal tags to the StringBuffer `source`.
appendBoolean2ArrayWithTags(StringBuffer, boolean[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional boolean array with start and end tag to the StringBuffer `source`.
appendBooleanArrayWithTags(StringBuffer, boolean[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded boolean array with equal tags to the StringBuffer `source`.
appendBooleanArrayWithTags(StringBuffer, boolean[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded boolean array with start and end tag to the StringBuffer `source`.
appendBooleanWithTags(StringBuffer, boolean, String) - Static method in class de.jstacs.io.XMLParser
  Appends a boolean value with equal tags to the StringBuffer `source` in the following way: "< `tag` > `b` < `/tag` >"
appendBooleanWithTags(StringBuffer, boolean, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a boolean value with start and end tag to the StringBuffer `source` in the following way: "< `startTag` > `b` < `/endTag` >"
appendByte2ArrayWithTags(StringBuffer, byte[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional byte array with equal tags to the StringBuffer `source`.
appendByte2ArrayWithTags(StringBuffer, byte[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional byte array with start and end tag to the StringBuffer `source`.
appendByteArrayWithTags(StringBuffer, byte[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded byte array with equal tags to the StringBuffer `source`.
appendByteArrayWithTags(StringBuffer, byte[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded byte array with start and end tag to the StringBuffer `source`.
appendByteWithTags(StringBuffer, byte, String) - Static method in class de.jstacs.io.XMLParser
  Appends a byte value with equal tags to the StringBuffer `source` in the following way: "< `tag` > `b` < `/tag` >"
appendByteWithTags(StringBuffer, byte, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a byte value with start and end tag to the StringBuffer `source` in the following way: "< `startTag` > `b` < `/endTag` >"
appendCollection(StringBuffer) - Method in class de.jstacs.parameters.CollectionParameter
  Appends the internal `ParameterSet` in its XML-representation (`ParameterSet.toXML()`) to `buf`
appendCollection(StringBuffer) - Method in class de.jstacs.parameters.EnumParameter
appendDouble2ArrayWithTags(StringBuffer, double[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional double array with equal tags to the StringBuffer `source`.
appendDouble2ArrayWithTags(StringBuffer, double[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional double array with start and end tag to the StringBuffer `source`.
appendDoubleArrayWithTags(StringBuffer, double[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded double array with equal tags to the StringBuffer `source`.
appendDoubleArrayWithTags(StringBuffer, double[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded double array with start and end tag to the StringBuffer `source`.
appendDoubleWithTags(StringBuffer, double, String) - Static method in class de.jstacs.io.XMLParser
  Appends a double value with equal tags to the StringBuffer `source` in the following way: "< `tag` > `d` < `/tag` >"
appendDoubleWithTags(StringBuffer, double, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a double value with start and end tag to the StringBuffer `source` in the following way: "< `startTag` > `d` < `/endTag` >"
appendEnumWithTags(StringBuffer, Enum<T>, String) - Static method in class de.jstacs.io.XMLParser
  Appends an Enum object with equal tags to the StringBuffer `source`.
appendEnumWithTags(StringBuffer, Enum<T>, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an Enum object with start and end tag to the StringBuffer `source`.
appendInt2ArrayWithTags(StringBuffer, int[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional int array with equal tags to the StringBuffer `source`.
appendInt2ArrayWithTags(StringBuffer, int[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional int array with start and end tag to the StringBuffer `source`.
appendIntArrayWithTags(StringBuffer, int[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded int array with equal tags to the StringBuffer `source`.
appendIntArrayWithTags(StringBuffer, int[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded int array with start and end tag to the StringBuffer `source`.
appendIntWithTags(StringBuffer, int, String) - Static method in class de.jstacs.io.XMLParser
  Appends an int value with equal tags to the StringBuffer `source` in the following way: "< `tag` > `i` < `/tag` >"
appendIntWithTags(StringBuffer, int, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an int value with start and end tag to the StringBuffer `source` in the following way: "< `startTag` > `i` < `/endTag` >"
appendLongWithTags(StringBuffer, long, String) - Static method in class de.jstacs.io.XMLParser
  Appends a long value with equal tags to the StringBuffer `source` in the following way: "< `tag` > `i` < `/tag` >"
appendLongWithTags(StringBuffer, long, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a long value with start and end tag to the StringBuffer `source` in the following way: "< `startTag` > `i` < `/endTag` >"
appendMainInfo(StringBuffer) - Method in class de.jstacs.results.Result
  This method can be used in the toXML-method to append the main information (name, comment, datatype).
appendStorable2ArrayWithTags(StringBuffer, Storable[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `Storable` array with equal tags to the StringBuffer `source`.
appendStorable2ArrayWithTags(StringBuffer, Storable[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional `Storable` array with start and end tag to the StringBuffer `source`.
appendStorable3ArrayWithTags(StringBuffer, Storable[][][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded three dimensional `Storable` array with equal tags to the StringBuffer `source`.
appendStorable3ArrayWithTags(StringBuffer, Storable[][][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded three dimensional `Storable` array with start and end tag to the StringBuffer `source`.
appendStorableArrayWithTags(StringBuffer, Storable[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded Storable array with equal tags to the StringBuffer `source`.
appendStorableArrayWithTags(StringBuffer, Storable[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded Storable array with start and end tag to the StringBuffer `source`.
appendStorableOrNullWithTags(StringBuffer, Storable, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `Storable` object or "null" with equal tags to the StringBuffer `source`.
appendStorableOrNullWithTags(StringBuffer, Storable, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `Storable` object or "null" with start and end tag to the StringBuffer `source`.
appendStorableWithTags(StringBuffer, Storable, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `Storable` object with equal tags to the StringBuffer `source`.
appendStorableWithTags(StringBuffer, Storable, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a `Storable` object with start and end tag to the StringBuffer `source`.
appendString2ArrayWithTags(StringBuffer, String[][], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional String array with equal tags to the StringBuffer `source`.
appendString2ArrayWithTags(StringBuffer, String[][], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded two dimensional String array with start and end tag to the StringBuffer `source`.
appendStringArrayWithTags(StringBuffer, String[], String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded String array with equal tags to the StringBuffer `source`.
appendStringArrayWithTags(StringBuffer, String[], String, String) - Static method in class de.jstacs.io.XMLParser
  Appends an encoded String array with start and end tag to the StringBuffer `source`.
appendStringWithTags(StringBuffer, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a String with equal tags to the StringBuffer `source` in the following way: "< `tag` > `s` < `/tag` >"
appendStringWithTags(StringBuffer, String, String, String) - Static method in class de.jstacs.io.XMLParser
  Appends a String with start and end tag to the StringBuffer `source` in the following way: "< `startTag` > `s` < `/endTag` >"
ArbitrarySequence - Class in de.jstacs.data.sequences
  The class for any continuous or hybrid sequence.
ArbitrarySequence(AlphabetContainer, double[]) - Constructor for class de.jstacs.data.sequences.ArbitrarySequence
  This constructor is designed for the method `AbstractModel.emitSample(int, int...)`.
ArbitrarySequence(AlphabetContainer, String) - Constructor for class de.jstacs.data.sequences.ArbitrarySequence
  Creates a new sequence from a string representation using the default delimiter.
ArbitrarySequence(AlphabetContainer, SequenceAnnotation[], String, String) - Constructor for class de.jstacs.data.sequences.ArbitrarySequence
  Creates a new sequence from a string representation using the delimiter `delim`.
ArbitrarySequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor) - Constructor for class de.jstacs.data.sequences.ArbitrarySequence
  Creates a new sequence from a `SymbolExtractor`.
ArrayHandler - Class in de.jstacs.io
  This class enables the user to cast and clone arrays easily.
ArrayHandler() - Constructor for class de.jstacs.io.ArrayHandler
ArrayParameterSet - Class in de.jstacs.parameters
  Class for a `ParameterSet` that consists of a length-`Parameter` that defines the length of the array and an array of `ParameterSetContainer`s of this length.
ArrayParameterSet(ParameterSet, String, String, String, String, NumberValidator<Integer>) - Constructor for class de.jstacs.parameters.ArrayParameterSet
  Creates a new `ArrayParameterSet` from a `Class` that can be instantiated using this `ArrayParameterSet` and templates for the `ParameterSet` in each element of the array, the name and the comment that are displayed for the `ParameterSetContainer`s enclosing the `ParameterSet`s.
ArrayParameterSet(ParameterSet, String, String) - Constructor for class de.jstacs.parameters.ArrayParameterSet
  Creates a new `ArrayParameterSet` from a `Class` that can be instantiated using this `ArrayParameterSet` and templates for the `ParameterSet` in each element of the array, the name and the comment that are displayed for the `ParameterSetContainer`s enclosing the `ParameterSet`s.
ArrayParameterSet(StringBuffer) - Constructor for class de.jstacs.parameters.ArrayParameterSet
  Creates a new `ArrayParameterSet` from its XML-representation.
assess(MeasureParameters, ClassifierAssessmentAssessParameterSet, Sample...) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment
  Assesses the contained classifiers.
assess(MeasureParameters, ClassifierAssessmentAssessParameterSet, ProgressUpdater, Sample...) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment
  Assesses the contained classifiers.
assess(MeasureParameters, ClassifierAssessmentAssessParameterSet, ProgressUpdater, Sample[][]...) - Method in class de.jstacs.classifier.assessment.ClassifierAssessment
  Assesses the contained classifiers.
assessWithPredefinedSplits(MeasureParameters, ClassifierAssessmentAssessParameterSet, ProgressUpdater, Sample[]...) - Method in class de.jstacs.classifier.assessment.KFoldCrossValidation
  This method implements a k-fold crossvalidation on previously split data.
AsymmetricTensor - Class in de.jstacs.algorithms.graphs.tensor
  This class can be used for `Tensor`s which are not symmetric, as opposed to the symmetry defined in `SymmetricTensor`.
AsymmetricTensor(int, byte) - Constructor for class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor
  This constructor creates an empty asymmetric tensor with given dimension.
AsymmetricTensor(double[][][], int, byte) - Constructor for class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor
  This constructor creates and checks a filled asymmetric tensor with given dimension.

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