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

A

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.
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 doubles.
AbstractScoreBasedClassifier.DoubleTableResult(StringBuffer) - Constructor for class de.jstacs.classifier.AbstractScoreBasedClassifier.DoubleTableResult
This is the constructor for Storable.
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 Constraints.
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 Parameters
addResults(MeanResultSet, MeanResultSet) - Static method in class de.jstacs.results.MeanResultSet
Adds two MeanResultsSets.
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 >"
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.InstanceParameterSet
The alphabet the model works on
Alphabet.AlphabetParameterSet - Class in de.jstacs.data
The super class for the ParameterSet of any Alphabet.
Alphabet.AlphabetParameterSet(Class<? extends Alphabet>) - Constructor for class de.jstacs.data.Alphabet.AlphabetParameterSet
Creates a new AlphabetParameterSet.
Alphabet.AlphabetParameterSet(StringBuffer) - Constructor for class de.jstacs.data.Alphabet.AlphabetParameterSet
Creates a new 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 AlphabetContainers.
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 AlphabetContainer from the StringBuffer.
AlphabetContainerParameterSet - Class in de.jstacs.data
Class for the ParameterSet of an AlphabetContainer.
AlphabetContainerParameterSet(boolean, 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 Alphabets.
AlphabetContainerParameterSet(Alphabet[], int[]) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet
Creates a new AlphabetContainerParameterSet from an array of Alphabets and an array of ints 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 Alphabets of defined length.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(boolean) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
Creates a new AlphabetArrayParameterSet from the information if the array shall contain only the parameters for discrete Alphabets.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
Creates a new AlphabetArrayParameterSet from its XML-representation.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[], boolean) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
Creates a new AlphabetArrayParameterSet from an array of Alphabets and the information if all alphabets are discrete
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet - Class in de.jstacs.data
Class for the parameters of an array of Alphabets where each alphabet may be used for one or more sections of positions.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(boolean) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
Creates a new SectionDefinedAlphabetParameterSet for a set of discrete or continuous alphabets.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[], int[], boolean) - Constructor for class de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
Creates a new SectionDefinedAlphabetParameterSet from an array of Alphabets, an array of indexes that define the index of the Alphabet<>/code> in alphabets/code> 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 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
alternativeInstanceClass - Variable in class de.jstacs.parameters.ParameterSet
The class that can be instantiated using this ParameterSet
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.
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.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 emitSample( int n ) of AbstractModel.
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 SymbolExctractor.
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 ParameterSetContainers of this length.
ArrayParameterSet(Class, 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 ParameterSetContainers enclosing the ParameterSets.
ArrayParameterSet(Class, 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 ParameterSetContainers enclosing the ParameterSets.
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
 
AsymmetricTensor - Class in de.jstacs.algorithms.graphs.tensor
This class can be used for Tensors which are not symmetric, as opposed to the symmetry defined in SymmetricTensor.
AsymmetricTensor(int, byte) - Constructor for class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor
 
AsymmetricTensor(double[][][], int, byte) - Constructor for class de.jstacs.algorithms.graphs.tensor.AsymmetricTensor
 

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