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A

AbstractADPAlgorithm<X,Y,R,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This is the most abstract ADP algorithm just implementing the forward calculation of the dynamic programming tables for an arbitrary grammar.
AbstractADPAlgorithm(Grammar<N>, Class<R>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
 
AbstractDerivableValueComparatorWrapper<V> - Class in de.citec.tcs.alignment.comparators
An abstract convenience implementation of the ValueComparator interface and the DerivableComparator interface.
AbstractDerivableValueComparatorWrapper(String, ValueType, DerivableComparator<V, V>) - Constructor for class de.citec.tcs.alignment.comparators.AbstractDerivableValueComparatorWrapper
 
AbstractDissimilarityClassifier - Class in de.citec.tcs.alignment.learning
This is a convenience extension of the DissimilarityClassifier interface, which already implements most of the functionality to make the implementation of DissimilarityClassifiers easier.
AbstractDissimilarityClassifier(int[]) - Constructor for class de.citec.tcs.alignment.learning.AbstractDissimilarityClassifier
 
AbstractHTMLColumn<X,Y> - Class in de.citec.tcs.alignment.visualization
This is a convenience abstract implementation of HTMLColumn for cases where the left-hand elements and the right-hand elements should be visualized side by side.
AbstractHTMLColumn(String, ElementHTMLVisualizer<X>, ElementHTMLVisualizer<Y>) - Constructor for class de.citec.tcs.alignment.visualization.AbstractHTMLColumn
 
AbstractStrictAlignmentAlgorithm<X,Y,R> - Class in de.citec.tcs.alignment
This is an abstract super class implementing the Needleman-Wunsch-Algorithm or Wagner-Fischer-Algorithm to compute a standard edit distance, also called Levenshtein-distance, on input sequences.
AbstractStrictAlignmentAlgorithm(Comparator<X, Y>, Class<R>) - Constructor for class de.citec.tcs.alignment.AbstractStrictAlignmentAlgorithm
 
AbstractStrictDTWAlgorithm<X,Y,R> - Class in de.citec.tcs.alignment
This is an abstract super class implementing the dynamic time warping (DTW) dissimilarity.
AbstractStrictDTWAlgorithm(Class<R>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
 
AbstractValue - Class in de.citec.tcs.alignment.sequence
This is a convenience implementation of the Value interface.
AbstractValue(ValueType) - Constructor for class de.citec.tcs.alignment.sequence.AbstractValue
 
AbstractValueComparatorWrapper<V> - Class in de.citec.tcs.alignment.comparators
An abstract convenience implementation of the ValueComparator interface.
AbstractValueComparatorWrapper(String, ValueType, Comparator<V, V>) - Constructor for class de.citec.tcs.alignment.comparators.AbstractValueComparatorWrapper
 
actualCompare(String, String) - Method in class de.citec.tcs.alignment.comparators.CharStatComparator
 
actualCompare(double[], double[]) - Method in class de.citec.tcs.alignment.comparators.EuclideanComparator
 
actualCompare(double[], double[]) - Method in class de.citec.tcs.alignment.comparators.L1NormComparator
 
actualCompare(String, String) - Method in class de.citec.tcs.alignment.comparators.NCDComparator
 
actualCompare(double[], double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanComparator
 
actualCompare(double[], double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
 
actualCompare(double[], double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedL1Comparator
 
actualCompare(double[], double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
 
actualCompare(X, Y) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
This has to return a distance between a and b with the following restrictions: The return value has to lie between 0 and 1. 1 means maximum dissimilarity between a and b. 0 means maximum similarity between a and b (especially it should be true that a = b implies a zero distance). distance(a,b) should be equal or at least close to distance(b,a)
actualCompare(X, X) - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
 
actualCompare(double[], double[]) - Method in class de.citec.tcs.alignment.comparators.ZeroNormComparator
 
add(int, double) - Method in class de.citec.tcs.alignment.comparators.ListGradient
 
addColumn(HTMLColumn<X, Y>) - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
Adds a HTMLColumn to this HTMLVisualizer and overrides any HTMLColumn previously associated with the same keyword.
addRule(N, ProductionRule<N>) - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
Adds a production rule to this grammar.
addTask(I) - Method in class de.citec.tcs.alignment.parallel.Engine
Adds the task with the given identifier to this Engine.
addTasks(I[]) - Method in class de.citec.tcs.alignment.parallel.Engine
Adds the tasks with the given identifiers to this Engine.
addTasks(Collection<I>) - Method in class de.citec.tcs.alignment.parallel.Engine
Adds the tasks with the given identifiers to this Engine.
AffineGrammar - Class in de.citec.tcs.alignment.adp
This grammar describes affine (and local) sequence alignment as described by Smith&Waterman (1981) and Gotoh (1982).
AffineGrammar() - Constructor for class de.citec.tcs.alignment.adp.AffineGrammar
Creates an instance of the affine grammar.
AffineGrammar(int) - Constructor for class de.citec.tcs.alignment.adp.AffineGrammar
Creates an instance of the affine grammar.
AffineGrammar.Nonterminal - Enum in de.citec.tcs.alignment.adp
These are the nonterminal symbols for the affine grammar.
AffineNormalizer - Class in de.citec.tcs.alignment.comparators
The affine normalizer just maps the range [min, max] linearly to the range [0,1].
AffineNormalizer(double, double) - Constructor for class de.citec.tcs.alignment.comparators.AffineNormalizer
 
Alignment<X,Y> - Class in de.citec.tcs.alignment
This class models an Alignment as it is given out by a strict alignment.
Alignment(List<Operation<X, Y>>, Comparator<X, Y>, List<X>, List<Y>, double) - Constructor for class de.citec.tcs.alignment.Alignment
 
Alignment(Comparator<X, Y>, List<X>, List<Y>, double) - Constructor for class de.citec.tcs.alignment.Alignment
 
Alignment(Alignment<X, Y>) - Constructor for class de.citec.tcs.alignment.Alignment
A copy constructor.
AlignmentAlgorithm<X,Y,R> - Interface in de.citec.tcs.alignment
This is the most generic AlignmentAlgorithm interface for all algorithms that provide some sort of alignment between two input sequences.
AlignmentList<X,Y> - Class in de.citec.tcs.alignment
This is a list-based datastructure accumulating multiple AlignmentPaths.
AlignmentList() - Constructor for class de.citec.tcs.alignment.AlignmentList
 
AlignmentMap<X,Y> - Class in de.citec.tcs.alignment
This is a Map-based datastructure implementing a mapping from scores to Alignments.
AlignmentMap() - Constructor for class de.citec.tcs.alignment.AlignmentMap
 
AlignmentSpecification - Class in de.citec.tcs.alignment.comparators
The alignment specification defines which keywords of the input sequences shall be used and which comparator is to be used to calculate the local distance between two values for that keyword.
AlignmentSpecification(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.comparators.AlignmentSpecification
Constructs a copy of the given other AlignmentSpecification.
AlignmentSpecification(NodeSpecification, ValueComparator[]) - Constructor for class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
AlignmentSpecification(NodeSpecification, String[], ValueComparator[]) - Constructor for class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
AlignmentSpecification(NodeSpecification, String[], ValueComparator[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
Alphabet - Class in de.citec.tcs.alignment.sequence
An alphabet is an ordered set of arbitrary symbols.
Alphabet(HashMap<String, Integer>) - Constructor for class de.citec.tcs.alignment.sequence.Alphabet
 
Alphabet(String) - Constructor for class de.citec.tcs.alignment.sequence.Alphabet
Constructor for symbols either encoded as single characters without delimiter or as strings with | as delimiter.
Alphabet(String[]) - Constructor for class de.citec.tcs.alignment.sequence.Alphabet
Constructs an IndexingScheme from a mapping of indices to strings.
ArrayGradient - Class in de.citec.tcs.alignment.comparators
A simple array implementation of the Gradient interface.
ArrayGradient(double[]) - Constructor for class de.citec.tcs.alignment.comparators.ArrayGradient
 
averageScore() - Method in class de.citec.tcs.alignment.AlignmentMap
Returns the average score according to the given weighting scheme.

C

calculate() - Method in class de.citec.tcs.alignment.parallel.Engine
Starts the actual, parallel computation.
calculateAlignment(List<X>, List<Y>) - Method in class de.citec.tcs.alignment.AbstractStrictAlignmentAlgorithm
 
calculateAlignment(List<X>, List<Y>) - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
 
calculateAlignment(List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
 
calculateAlignment(List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm
 
calculateAlignment(List<X>, List<Y>) - Method in interface de.citec.tcs.alignment.AlignmentAlgorithm
This calculates the alignment dissimilarity D between the Sequences x ∈ X* and y ∈ Y* and returns it as an instance of the result class for this algorithm.
calculateComparatorDistances(OperationType, Node, Node) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
Calculates the distances returned by every single Comparator in this AlignmentSpecification.
calculateCompressedSize(String) - Method in enum de.citec.tcs.alignment.comparators.NCDComparator.CompressorType
Calculates the compressed size of the given input string in bytes.
calculateDerivative(AlignmentAlgorithm<Node, Node, ? extends DerivableAlignmentDistance<Node, Node>>, Sequence, Sequence) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
Calculates the alignment derivative between the two given input sequences using the given algorithm.
calculateDerivatives(AlignmentAlgorithm<Node, Node, R>, Sequence[], int) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
Calculates the pairwise alignment derivative between all given input sequences using the given algorithm.
calculateLMNNCostFunction(TreeSet<DistanceIndex>, double[]) - Method in class de.citec.tcs.alignment.learning.LMNNClassifier
Calculates the LMNN cost function given the target neighbors of some data point and its distances to the training data points.
calculateLMNNCostFunctionTest(int, double[]) - Method in class de.citec.tcs.alignment.learning.LMNNClassifier
Calculates the value of the LMNN cost function for the given data point, assuming that it belongs to the class with the given label and that it has the given distances to all training data points.
calculateLMNNCostFunctionTraining(int, int, double[]) - Method in class de.citec.tcs.alignment.learning.LMNNClassifier
Calculates the value of the LMNN cost function for the given data point, assuming that it belongs to the class with the given label and that it has the given distances to all training data points.
calculateNCD(String, String) - Method in class de.citec.tcs.alignment.comparators.NCDComparator
Returns the normalized compression distance between two input strings according to the compressor currently set.
calculateSoftminDerivatives(double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
Calculates the softmin'(x_i) function for all variables x_i in the given input.
calculateSoftminDerivatives(double, double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
Calculates the softmin'(x_i) function for all variables x_i in the given input.
calculateSoftminProbabilities(double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
Calculates the softmin probabilities p_i for the given beta and the given variables.
calculateSoftminProbabilities(double, double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
Calculates the softmin probabilities p_i for the given beta and the given variables.
calculateTestAccuracy(int[], double[][]) - Method in class de.citec.tcs.alignment.learning.AbstractDissimilarityClassifier
 
calculateTestAccuracy(int[], double[][]) - Method in interface de.citec.tcs.alignment.learning.DissimilarityClassifier
Returns the test accuracy given the distances between test data points and training data points as well as the true labels of the test data points.
calculateTrainingAccuracy(double[][]) - Method in class de.citec.tcs.alignment.learning.AbstractDissimilarityClassifier
 
calculateTrainingAccuracy(double[][]) - Method in interface de.citec.tcs.alignment.learning.DissimilarityClassifier
Returns the training accuracy given the distance matrix on the training set.
calculateVotes(double[]) - Method in class de.citec.tcs.alignment.learning.KNNClassifier
Returns the number of data points within the k nearest neighbors to the reference data point, that had some given class label.
calculateVotes(int, double[]) - Method in class de.citec.tcs.alignment.learning.KNNClassifier
Returns the number of data points within the k nearest neighbors to the reference data point, that had some given class label.
calculateWeighting(List<Double>) - Method in enum de.citec.tcs.alignment.DissimilarityWeighting
 
calculateWeighting(double[]) - Method in enum de.citec.tcs.alignment.DissimilarityWeighting
This calculates the normalized weights (between 0 and 1 and adding up to 1) for the given dissimilarities.
CharacterVisualizer - Class in de.citec.tcs.alignment.visualization
This is a visualizer for alignments of Strings, that is: List of Characters.
CharacterVisualizer() - Constructor for class de.citec.tcs.alignment.visualization.CharacterVisualizer
 
CharStatComparator - Class in de.citec.tcs.alignment.comparators
This compares strings using statistics over the number of letters inside.
CharStatComparator() - Constructor for class de.citec.tcs.alignment.comparators.CharStatComparator
 
checkValidity(Grammar, Comparator) - Static method in class de.citec.tcs.alignment.adp.ComparatorValidator
Checks whether the given Comparator supports all OperationType the given Grammar requires and returns an IllegalArgumentException if it does not.
checkValidity(AlignmentAlgorithm<X, Y, ?>, Comparator<? extends X, ? extends Y>) - Static method in class de.citec.tcs.alignment.ComparatorValidator
Checks whether the given Comparator supports all OperationType the given AlignmentAlgorithm requires and returns an IllegalArgumentException if it does not.
choice(double[]) - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
This should implement the choice function as the term is used in the Bellman's Gap context.
choice(double[]) - Method in class de.citec.tcs.alignment.adp.SoftADPFullAlgorithm
 
choice(double[]) - Method in class de.citec.tcs.alignment.adp.SoftADPScoreAlgorithm
 
choice(double[]) - Method in class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm
This should implement the choice function as the term is used in the Bellman's Gap context.
choice(double[]) - Method in class de.citec.tcs.alignment.adp.SparseStrictADPFullAlgorithm
 
choice(double[]) - Method in class de.citec.tcs.alignment.adp.SparseStrictADPScoreAlgorithm
 
choice(double[]) - Method in class de.citec.tcs.alignment.adp.StrictADPCooptimalAlgorithm
 
choice(double[]) - Method in class de.citec.tcs.alignment.adp.StrictADPFullAlgorithm
 
choice(double[]) - Method in class de.citec.tcs.alignment.adp.StrictADPScoreAlgorithm
 
classifyTest(double[]) - Method in class de.citec.tcs.alignment.learning.AbstractDissimilarityClassifier
 
classifyTest(double[]) - Method in interface de.citec.tcs.alignment.learning.DissimilarityClassifier
Returns the supposed class label for some data point, that is not part of the training set, based on its distances to the training data set.
classifyTest(double[]) - Method in class de.citec.tcs.alignment.learning.KNNClassifier
 
classifyTest(double[]) - Method in class de.citec.tcs.alignment.learning.LMNNClassifier
 
classifyTraining(int, double[]) - Method in class de.citec.tcs.alignment.learning.AbstractDissimilarityClassifier
 
classifyTraining(int, double[]) - Method in interface de.citec.tcs.alignment.learning.DissimilarityClassifier
Returns the supposed class label for some data point in the training set based on its distances to all training data points.
classifyTraining(int, double[]) - Method in class de.citec.tcs.alignment.learning.KNNClassifier
 
classifyTraining(int, double[]) - Method in class de.citec.tcs.alignment.learning.LMNNClassifier
 
clearTasks() - Method in class de.citec.tcs.alignment.parallel.Engine
Removes all tasks from this Engine.
CommandLineProgressReporter - Class in de.citec.tcs.alignment.parallel
This is a default ProgressReporter that writes a notification to the command line after progressReportStepSize percent of computation are finished.
CommandLineProgressReporter() - Constructor for class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
 
Comparator<X,Y> - Interface in de.citec.tcs.alignment.comparators
Let X and Y be two arbitrary sets (corresponding to the generic type parameters of this class).
ComparatorValidator - Class in de.citec.tcs.alignment.adp
This class has the sole purpose to validate that a Comparator supports all OperationTypes a Grammar requires.
ComparatorValidator - Class in de.citec.tcs.alignment
This class has the sole purpose to validate that a Comparator supports all OperationTypes an AlignmentAlgorithm requires.
compare(OperationType, Node, Node) - Method in class de.citec.tcs.alignment.comparators.AbstractValueComparatorWrapper
 
compare(OperationType, Node, Node) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
compare(OperationType, X, Y) - Method in interface de.citec.tcs.alignment.comparators.Comparator
This method returns a dissimilarity between x and y using the alignment operation op with the following restrictions: compare(op,x,y) ≥ 0 (non-negativity) compare(op,x,y) ≤ 1 (normalization) x = y ⇒ compare(op,x,y) = 0 (equality) Further, this function guarantees consistency with respect to null inputs, that is, for any operation op ∈ {REPLACEMENT, DELETIONREPLACEMENT, INSERTIONREPLACEMENT} it holds: d(op, x, null) = d(DELETION, x, null) d(op, null, y) = d(INSERTION, null, y) and for any operation it holds: d(op, null, null) = 0 Please note that a and b might be null if this alignment uses gaps or skips.
compare(OperationType, X, Y) - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
compare(OperationType, X, Y) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
compare(OperationType, X, X) - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
compareTo(DPCellId) - Method in class de.citec.tcs.alignment.adp.DPCellId
 
compareTo(DistanceIndex) - Method in class de.citec.tcs.alignment.learning.DistanceIndex
 
compareTo(MatrixEngine.MatrixCoordinate) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine.MatrixCoordinate
 
ComparisonBasedSkipExtendedComparator<X,Y> - Class in de.citec.tcs.alignment.comparators
This is an abstract class providing - in addition to the constant gap and skip costs provided by the SkipExtendedComparator - the possibility to define gap and skip costs with respect to a constant element from both input sets.
ComparisonBasedSkipExtendedComparator(Y, X, Y, X) - Constructor for class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
ComparisonBasedSkipExtendedComparator(Y, X) - Constructor for class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
computeComparisonGradient(double[], double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
 
computeComparisonGradient(double[], double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
 
computeComparisonGradient(X, Y) - Method in class de.citec.tcs.alignment.comparators.ParameterLessComparisonBasedSkipExtendedComparator
 
computeComparisonGradient(X, Y) - Method in class de.citec.tcs.alignment.comparators.ParameterLessSkipExtendedComparator
 
computeComparisonGradient(X, Y) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
Computes the gradient of the comparator function w.r.t.
computeComparisonGradient(X, X) - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
 
computeGradient(DerivableComparator<X, Y>) - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
 
computeGradient(DerivableComparator<X, Y>) - Method in class de.citec.tcs.alignment.Alignment
 
computeGradient(DerivableComparator<X, Y>) - Method in class de.citec.tcs.alignment.AlignmentList
 
computeGradient(DerivableComparator<X, Y>) - Method in class de.citec.tcs.alignment.AlignmentMap
 
computeGradient(OperationType, Node, Node) - Method in class de.citec.tcs.alignment.comparators.AbstractDerivableValueComparatorWrapper
 
computeGradient(OperationType, Node, Node) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
computeGradient(OperationType, X, Y) - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
computeGradient(OperationType, X, Y) - Method in interface de.citec.tcs.alignment.comparators.DerivableComparator
Computes the gradient of this comparator function w.r.t.
computeGradient(OperationType, X, Y) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
computeGradient(OperationType, X, X) - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
computeGradient(DerivableComparator<X, Y>) - Method in class de.citec.tcs.alignment.CooptimalModel
 
computeGradient(DerivableComparator<X, Y>) - Method in interface de.citec.tcs.alignment.DerivableAlignmentDistance
This computes the gradient of this DerivableAlignmentDistance w.r.t.
computeGradient(DerivableComparator<X, X>, double[][]) - Method in class de.citec.tcs.alignment.learning.LMNNGradientCalculator
Calculates the gradient of the LMNN cost function with respect to the parameters of the given comparator.
CooptimalModel<X,Y> - Class in de.citec.tcs.alignment
This is a sparse model of all co-optimal paths in an alignment matrix.
CooptimalModel(Comparator<X, Y>, List<X>, List<Y>, double) - Constructor for class de.citec.tcs.alignment.CooptimalModel
 
costMatrixToVector(double[][]) - Static method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
Turns a cost matrix Lambda into vector form, where all rows are concatenated.
createCallable(I) - Method in class de.citec.tcs.alignment.parallel.Engine
A method that should create a Callable (computation job) for the given identifier object.
createCallable(MatrixEngine.MatrixCoordinate) - Method in class de.citec.tcs.alignment.ParallelGradientEngine
 
createCallable(MatrixEngine.MatrixCoordinate) - Method in class de.citec.tcs.alignment.ParallelProcessingEngine
 
createCallable(MatrixEngine.MatrixCoordinate) - Method in class de.citec.tcs.alignment.SquareParallelProcessingEngine
 
createGenericMatrix(int, int, Class<X>) - Static method in class de.citec.tcs.alignment.parallel.MatrixEngine
This is a helper method that creates an object matrix of the given class.
CSVExporter - Class in de.citec.tcs.alignment.csv
This class holds methods to export a Sequence to a CSV file, along with its NodeSpecification, which can be exported to a JSON file.
CSVImporter - Class in de.citec.tcs.alignment.csv
This class holds methods to import a Sequence from a given CSV file, and an according NodeSpecification from a given JSON file.
currentParameterIndex() - Method in class de.citec.tcs.alignment.comparators.ArrayGradient
 
currentParameterIndex() - Method in class de.citec.tcs.alignment.comparators.EmptyGradient
 
currentParameterIndex() - Method in interface de.citec.tcs.alignment.comparators.Gradient
The index of the parameter of the current gradient entry.
currentParameterIndex() - Method in class de.citec.tcs.alignment.comparators.ListGradient
 
currentParameterIndex() - Method in class de.citec.tcs.alignment.comparators.SingletonGradient
 
currentValue() - Method in class de.citec.tcs.alignment.comparators.ArrayGradient
 
currentValue() - Method in class de.citec.tcs.alignment.comparators.EmptyGradient
 
currentValue() - Method in interface de.citec.tcs.alignment.comparators.Gradient
The current gradient value.
currentValue() - Method in class de.citec.tcs.alignment.comparators.ListGradient
 
currentValue() - Method in class de.citec.tcs.alignment.comparators.SingletonGradient
 

D

de.citec.tcs.alignment - package de.citec.tcs.alignment
This module defines the interface for AlignmentAlgorithms as well as some helper classes.
de.citec.tcs.alignment.adp - package de.citec.tcs.alignment.adp
This package contains a more general approach to construct AlignmentAlgorithms by relying on the theoretical concept of Algebraic Dynamic Programming (ADP) as developed by Giegerich et al.
de.citec.tcs.alignment.comparators - package de.citec.tcs.alignment.comparators
This module defines the interfaces for Comparators in the TCS Alignment Toolbox.
de.citec.tcs.alignment.csv - package de.citec.tcs.alignment.csv
This module permits exporting and importing of Sequence objects to CSV files.
de.citec.tcs.alignment.learning - package de.citec.tcs.alignment.learning
This module is a custom implementation of the Large Margin Nearest Neighbor classification scheme of Weinberger, Saul, et al.
de.citec.tcs.alignment.parallel - package de.citec.tcs.alignment.parallel
This module provides a very basic support for the parallel computing of tasks (Engine class) and entries of a matrix (MatrixEngine).
de.citec.tcs.alignment.primitives - package de.citec.tcs.alignment.primitives
This module contains convenience functions to interface with primitive datatypes more comfortably.
de.citec.tcs.alignment.sequence - package de.citec.tcs.alignment.sequence
This module contains the sequence datastructure of the TCS Alignment Toolbox.
de.citec.tcs.alignment.visualization - package de.citec.tcs.alignment.visualization
This module contains means to visualize Alignments.
de.citec.tcs.alignment.wrappers - package de.citec.tcs.alignment.wrappers
This module contains some wrappers to make usage of the TCSAlignmentToolbox easier.
DEFAULT_ALIGNMENT_LIMIT - Static variable in class de.citec.tcs.alignment.StrictAlignmentAllOptimalAlgorithm
 
DEFAULT_DELIMITER - Static variable in class de.citec.tcs.alignment.csv.CSVExporter
 
DEFAULT_NUMBER_OF_THREADS - Static variable in class de.citec.tcs.alignment.parallel.Engine
 
DEFAULT_PROGRESS_REPORT_STEP_SIZE - Static variable in class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
 
DEFAULT_SRC_LENGTH_LIMIT - Static variable in class de.citec.tcs.alignment.visualization.SourceCodeColumn
 
DEFAULTALPHABET - Static variable in class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
 
DEFAULTAPPROXTHRESHOLD - Static variable in class de.citec.tcs.alignment.Softmin
This means that softmin arguments with a weight smaller than 10^-3 will be disregarded.
DEFAULTBETA - Static variable in class de.citec.tcs.alignment.Softmin
 
DEFAULTKEYWORD - Static variable in class de.citec.tcs.alignment.sequence.Sequence
 
Defaults - Class in de.citec.tcs.alignment.comparators
This is a class with convenience methods that provide sensible default comparators for given KeywordSpecifications.
Defaults() - Constructor for class de.citec.tcs.alignment.comparators.Defaults
 
DEFAULTSTRINGLENGTH - Static variable in class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
 
DEFAULTVECTORIALLENGTH - Static variable in class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
 
dependencySort() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
 
dependencySort() - Method in class de.citec.tcs.alignment.adp.DTWGrammar
 
dependencySort() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
 
dependencySort() - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
 
dependencySort() - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
 
dependencySort() - Method in interface de.citec.tcs.alignment.adp.Grammar
Returns the nonterminals of this grammar sorted according to their dependencies on one another.
dependencySort() - Method in class de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar
 
DerivableAlignmentDistance<X,Y> - Interface in de.citec.tcs.alignment
This is an interface to provide calculation methods for the gradient of an alignment w.r.t.
DerivableComparator<X,Y> - Interface in de.citec.tcs.alignment.comparators
This is an interface for comparators that have derivable parameters.
DerivableStringComparatorWrapper - Class in de.citec.tcs.alignment.comparators
This is a wrapper for Comparators on StringValues.
DerivableStringComparatorWrapper(String, DerivableComparator<String, String>) - Constructor for class de.citec.tcs.alignment.comparators.DerivableStringComparatorWrapper
 
DerivableSymbolicComparatorWrapper - Class in de.citec.tcs.alignment.comparators
This is a wrapper for Comparators on SymbolicValues.
DerivableSymbolicComparatorWrapper(String, DerivableComparator<String, String>) - Constructor for class de.citec.tcs.alignment.comparators.DerivableSymbolicComparatorWrapper
 
DerivableVectorialComparatorWrapper - Class in de.citec.tcs.alignment.comparators
This is a wrapper for Comparators on VectorialValues.
DerivableVectorialComparatorWrapper(String, DerivableComparator<double[], double[]>) - Constructor for class de.citec.tcs.alignment.comparators.DerivableVectorialComparatorWrapper
 
DissimilarityClassifier - Interface in de.citec.tcs.alignment.learning
This is an interface for dissimilarity based classifiers, that is: Classifiers that are able to provide an estimate of the most likely class label for some given, unseen data point based on their dissimilarities to some set of training data points for which the true label is known.
DissimilarityWeighting - Enum in de.citec.tcs.alignment
This is a helper class to enable users to weight a collection of dissimilarities based on different schemes specified below.
distance(String, String) - Static method in class de.citec.tcs.alignment.comparators.CharStatComparator
This calculates the distance between the two strings a and b calculating for each alphanumeric character (a-z, 0-9) the number of times it occured in both strings at taking the difference of both.
distance(double[], double[]) - Static method in class de.citec.tcs.alignment.comparators.EuclideanComparator
Returns the Euclidian distance between the vectors a and b, given that they have the same length.
distance(double[], double[]) - Static method in class de.citec.tcs.alignment.comparators.L1NormComparator
Returns the euclidian distance between the vectors a and b, given that they have the same length.
distance(double[], double[], double[]) - Static method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
Returns the relevance-weighted Euclidian distance between the vectors a and b, given that they have the same length.
distance(double[], double[], double[]) - Static method in class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
Returns the relevance-weighted L1 distance between the vectors a and b, given that they have the same length.
distance(double[], double[]) - Static method in class de.citec.tcs.alignment.comparators.ZeroNormComparator
Calculates the zero norm distance between both input vectors, which is equivalent to the number of unequal elements.
distance - Variable in class de.citec.tcs.alignment.learning.DistanceIndex
 
DistanceIndex - Class in de.citec.tcs.alignment.learning
 
DistanceIndex(int, double) - Constructor for class de.citec.tcs.alignment.learning.DistanceIndex
 
DistanceIndex.AndFilter - Class in de.citec.tcs.alignment.learning
Returns true if and only if both underlying filters return true.
DistanceIndex.AndFilter(DistanceIndex.IndexFilter, DistanceIndex.IndexFilter) - Constructor for class de.citec.tcs.alignment.learning.DistanceIndex.AndFilter
 
DistanceIndex.IdentityFilter - Class in de.citec.tcs.alignment.learning
This filter returns true if the input index is equal to the reference index.
DistanceIndex.IdentityFilter(int) - Constructor for class de.citec.tcs.alignment.learning.DistanceIndex.IdentityFilter
 
DistanceIndex.IndexFilter - Interface in de.citec.tcs.alignment.learning
This is an interface for functions that filter indices.
DistanceIndex.Labelfilter - Class in de.citec.tcs.alignment.learning
Returns true if and only if the label of the input data point is the same as the reference label.
DistanceIndex.Labelfilter(int, int[]) - Constructor for class de.citec.tcs.alignment.learning.DistanceIndex.Labelfilter
 
DistanceIndex.NotFilter - Class in de.citec.tcs.alignment.learning
Returns true if and only if the underlying filter returns false.
DistanceIndex.NotFilter(DistanceIndex.IndexFilter) - Constructor for class de.citec.tcs.alignment.learning.DistanceIndex.NotFilter
 
Doubles - Class in de.citec.tcs.alignment.primitives
This class provides static functions to transform double arrays to lists of doubles.
DPCellId - Class in de.citec.tcs.alignment.adp
This identifies a cell in the dynamic programming tables by the ordinal of the nonterminal symbol, the index in the left sequence (i) and the index in the right sequence (j).
DPCellId(int, int, int) - Constructor for class de.citec.tcs.alignment.adp.DPCellId
 
DTWGrammar - Class in de.citec.tcs.alignment.adp
This is a grammar for dynamic time warping.
DTWGrammar() - Constructor for class de.citec.tcs.alignment.adp.DTWGrammar
 
DTWGrammar.Nonterminal - Enum in de.citec.tcs.alignment.adp
 

E

ElementHTMLVisualizer<X> - Interface in de.citec.tcs.alignment.visualization
This is an interface for functions that are able to visualize single elements
EmptyGradient - Class in de.citec.tcs.alignment.comparators
A trivial Gradient implementation without any entries.
EmptyGradient() - Constructor for class de.citec.tcs.alignment.comparators.EmptyGradient
 
ENCODING - Static variable in class de.citec.tcs.alignment.visualization.CharacterVisualizer
 
endColumn - Variable in class de.citec.tcs.alignment.visualization.SourceCodeColumn.CodePosition
 
endLine - Variable in class de.citec.tcs.alignment.visualization.SourceCodeColumn.CodePosition
 
Engine<I extends Comparable<I>,R> - Class in de.citec.tcs.alignment.parallel
This is an abstract parent class to calculate generic jobs in parallel and handle their messages.
Engine(Class<I>, Class<R>) - Constructor for class de.citec.tcs.alignment.parallel.Engine
 
Engine.CalculationResult<I,R> - Class in de.citec.tcs.alignment.parallel
This is a helper class to store results of parallel computations.
Engine.CalculationResult(I, R) - Constructor for class de.citec.tcs.alignment.parallel.Engine.CalculationResult
 
entries(int, int) - Method in class de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar
 
entries(int, int) - Method in interface de.citec.tcs.alignment.adp.SparseGrammar
 
equals(Object) - Method in class de.citec.tcs.alignment.adp.DPCellId
 
equals(Object) - Method in class de.citec.tcs.alignment.adp.ProductionRule
 
equals(Object) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
equals(Object) - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
equals(Object) - Method in class de.citec.tcs.alignment.comparators.EuclideanComparator
 
equals(Object) - Method in class de.citec.tcs.alignment.comparators.ExponentialNormalizer
 
equals(Object) - Method in class de.citec.tcs.alignment.comparators.HyperbolicNormalizer
 
equals(Object) - Method in class de.citec.tcs.alignment.comparators.L1NormComparator
 
equals(Object) - Method in class de.citec.tcs.alignment.comparators.NCDComparator
 
equals(Object) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
equals(Object) - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
equals(Object) - Method in class de.citec.tcs.alignment.learning.DistanceIndex
 
equals(Object) - Method in class de.citec.tcs.alignment.Operation
 
equals(Object) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine.MatrixCoordinate
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.AbstractValue
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.KeywordSpecification
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.Node
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.NodeSpecification
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.Sequence
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.StringValue
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.SymbolicValue
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.VectorialKeywordSpecification
 
equals(Object) - Method in class de.citec.tcs.alignment.sequence.VectorialValue
 
EuclideanComparator - Class in de.citec.tcs.alignment.comparators
Compares vectors using the L2-Norm.
EuclideanComparator(int) - Constructor for class de.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(Normalizer, int) - Constructor for class de.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(int, double) - Constructor for class de.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(Normalizer, int, double) - Constructor for class de.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(double[], double[], double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(Normalizer, double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(Normalizer, double[], double[], double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.EuclideanComparator
 
ExponentialNormalizer - Class in de.citec.tcs.alignment.comparators
This normalizes by using the function 1-exp(-beta*d)
ExponentialNormalizer(double) - Constructor for class de.citec.tcs.alignment.comparators.ExponentialNormalizer
 
ExponentialNormalizer() - Constructor for class de.citec.tcs.alignment.comparators.ExponentialNormalizer
 
exportNodeSpecification(NodeSpecification, String) - Static method in class de.citec.tcs.alignment.csv.CSVExporter
This exports a NodeSpecification to a JSON file.
exportNodeSpecification(NodeSpecification, File) - Static method in class de.citec.tcs.alignment.csv.CSVExporter
This exports a NodeSpecification to a JSON file.
exportNodeSpecification(NodeSpecification, Writer) - Static method in class de.citec.tcs.alignment.csv.CSVExporter
This exports a NodeSpecification to a Writer.
exportSequence(Sequence, String) - Static method in class de.citec.tcs.alignment.csv.CSVExporter
This exports a sequence to a file of comma-separated values (CSV).
exportSequence(Sequence, File) - Static method in class de.citec.tcs.alignment.csv.CSVExporter
This exports a sequence to a file of comma-separated values (CSV).
exportSequence(Sequence, Writer) - Static method in class de.citec.tcs.alignment.csv.CSVExporter
This exports a sequence to a Writer as CSV data.
exportSequence(Sequence, String, String) - Static method in class de.citec.tcs.alignment.csv.CSVExporter
This exports a sequence to a CSV file, with a specified delimiter-string.
exportSequence(Sequence, File, String) - Static method in class de.citec.tcs.alignment.csv.CSVExporter
This exports a sequence to a CSV file, with a specified delimiter-string.
exportSequence(Sequence, Writer, String) - Static method in class de.citec.tcs.alignment.csv.CSVExporter
This exports a sequence to a CSV file, with a specified delimiter-string.
extractCodePosition(X) - Method in interface de.citec.tcs.alignment.visualization.SourceCodeColumn.PositionExtractor
Extracts the CodePosition from a given object.
extractNumberOfColumns(R[][]) - Static method in class de.citec.tcs.alignment.parallel.MatrixEngine
Returns the number of columns in the given matrix and checks if the number of columns is consistent, that is: if the given input-array is indeed a matrix.
extractValue(Node) - Method in class de.citec.tcs.alignment.comparators.AbstractValueComparatorWrapper
 

F

filter(int) - Method in class de.citec.tcs.alignment.learning.DistanceIndex.AndFilter
Returns true if and only if both underlying filters return true.
filter(int) - Method in class de.citec.tcs.alignment.learning.DistanceIndex.IdentityFilter
Returns true if and only if the input index is equal to the reference index.
filter(int) - Method in interface de.citec.tcs.alignment.learning.DistanceIndex.IndexFilter
Returns true if the data point with the given index should be considered and false if it should not be considered.
filter(int) - Method in class de.citec.tcs.alignment.learning.DistanceIndex.Labelfilter
Returns true if and only if the label of the input data point is the same as the reference label.
filter - Variable in class de.citec.tcs.alignment.learning.DistanceIndex.NotFilter
 
filter(int) - Method in class de.citec.tcs.alignment.learning.DistanceIndex.NotFilter
Returns true if and only if the underlying filter returns false.
FlexibleGrammar<N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This is a flexible grammar implementation that allows users to create new grammars at runtime.
FlexibleGrammar(Class<N>, N) - Constructor for class de.citec.tcs.alignment.adp.FlexibleGrammar
 
FlexibleGrammar.RuleAvailabilityMatrix<N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
 
FlexibleGrammar.RuleAvailabilityMatrix(int, int) - Constructor for class de.citec.tcs.alignment.adp.FlexibleGrammar.RuleAvailabilityMatrix
 

G

generateSequences(int, int, int) - Static method in class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
This generates N random sequences of length L each with K keywords.
generateSequences(int, int, NodeSpecification) - Static method in class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
This generates N random sequences of length L each according to the given NodeSpecification.
generateSpecification(int) - Static method in class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
This generates an AlignmentSpecification and implicitly a NodeSpecification for K keywords.
getAccepting() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
 
getAccepting() - Method in class de.citec.tcs.alignment.adp.DTWGrammar
 
getAccepting() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
 
getAccepting() - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
 
getAccepting() - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
 
getAccepting() - Method in interface de.citec.tcs.alignment.adp.Grammar
Returns the set of all accepting nonterminals of this grammar.
getAccepting() - Method in class de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar
 
getActualComparator() - Method in class de.citec.tcs.alignment.comparators.AbstractDerivableValueComparatorWrapper
 
getAlignments(double) - Method in class de.citec.tcs.alignment.AlignmentMap
Returns all Alignments for the given score.
getAllAlignments() - Method in class de.citec.tcs.alignment.AlignmentMap
Returns all Alignments stored in this map in order of their score (from good/low to bad/high).
getAlpha() - Method in class de.citec.tcs.alignment.comparators.HyperbolicNormalizer
 
getAlphabet() - Method in class de.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
Returns the Alphabet that defines which symbols are allowed for this keyword.
getAlphabet() - Method in class de.citec.tcs.alignment.sequence.SymbolicValue
Returns the Alphabet that defines which symbols are allowed for this keyword.
getAvailabilities(int, int) - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
 
getAvailabilityIndices() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar.RuleAvailabilityMatrix
 
getAxiom() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
 
getAxiom() - Method in class de.citec.tcs.alignment.adp.DTWGrammar
 
getAxiom() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
 
getAxiom() - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
 
getAxiom() - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
 
getAxiom() - Method in interface de.citec.tcs.alignment.adp.Grammar
Returns the axiom of this grammar.
getAxiom() - Method in class de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar
 
getBeta() - Method in class de.citec.tcs.alignment.comparators.ExponentialNormalizer
 
getColumn(String) - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
Returns the index of the HTMLColumn belonging to the given keyword or -1 if no HTMLColumn for that keyword exists.
getColumns() - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
Returns all HTMLColumns this HTMLVisualizer will visualize ordered according to their keyword.
getComparator() - Method in class de.citec.tcs.alignment.AbstractStrictAlignmentAlgorithm
 
getComparator() - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
 
getComparator() - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
 
getComparator() - Method in class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm
 
getComparator() - Method in interface de.citec.tcs.alignment.AlignmentAlgorithm
This should return the Comparator used to compute local distances for this algorithm.
getComparator(String) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
Returns the Comparator that is currently set for the given keyword.
getComparator(int) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
Returns the Comparator that is currently set for the given keyword.
getComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
 
getComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
 
getComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.ParameterLessComparisonBasedSkipExtendedComparator
 
getComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.ParameterLessSkipExtendedComparator
 
getComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
Return the current value of all parameters of this comparator.
getComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
 
getCooptimals() - Method in class de.citec.tcs.alignment.CooptimalModel
A Map of matrix coordinates to an array of sequences of operations that can be co-optimally applied at the given position of the dynamic programming matrix.
getCSS() - Method in class de.citec.tcs.alignment.visualization.AbstractHTMLColumn
This default implementation returns an empty string.
getCSS() - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
This method should return CSS code containing styling rules for this column.
getCSS() - Method in class de.citec.tcs.alignment.visualization.SourceCodeColumn
 
getDefaultComparator(KeywordSpecification) - Static method in class de.citec.tcs.alignment.comparators.Defaults
Returns a sensible default comparator for the given KeywordSpecification.
getDefaultComparators(KeywordSpecification[]) - Static method in class de.citec.tcs.alignment.comparators.Defaults
Returns sensible default comparators for the given KeywordSpecifications.
getDefaultComparators(NodeSpecification) - Static method in class de.citec.tcs.alignment.comparators.Defaults
Returns sensible default comparators for the given NodeSpecification, one for each contained KeywordSpecification.
getDefaultReplacementMatrix(int) - Static method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
Creates a default Lambda replacement matrix for an alphabet of size N.
getDeletions() - Static method in enum de.citec.tcs.alignment.comparators.OperationType
Returns an array containing the Deletion OperationTypes, namely DELETION and SKIPDELETION.
getDifference(Alignment<Node, Node>) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Returns the difference at each operation of the given AlignmentPath.
getDistance() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
 
getDistance() - Method in class de.citec.tcs.alignment.Alignment
 
getDistance() - Method in class de.citec.tcs.alignment.AlignmentList
Returns the average distance of all stored paths.
getDistance() - Method in class de.citec.tcs.alignment.AlignmentMap
Returns the average distance of all stored Alignments.
getDistance() - Method in class de.citec.tcs.alignment.CooptimalModel
 
getDistance() - Method in interface de.citec.tcs.alignment.DerivableAlignmentDistance
Returns the distance between the two input sequences.
getDistances() - Method in class de.citec.tcs.alignment.ParallelGradientEngine
Returns the DerivableAlignmentDistance objects used for derivative calculation.
getDoubleResultMatrix() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
Returns the results of the calculation as a primitive double matrix.
getExtensions(Alignment<Node, Node>) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Returns the sequence extensions modelled by this AlignmentPath.
getGaps() - Static method in enum de.citec.tcs.alignment.comparators.OperationType
Returns an array containing the gap OperationTypes, namely DELETION and INSERTION.
getHTML(Operation<X, Y>) - Method in class de.citec.tcs.alignment.visualization.AbstractHTMLColumn
 
getHTML(Operation<X, Y>) - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
This method should return one or multiple td-tags (corresponding to the return value of getNumColumns()) containing the additional information for the given alignment Operation.
getImposters(int, double[], int[], double) - Static method in class de.citec.tcs.alignment.learning.DistanceIndex
Returns the indices of all data points from other classes, that are closer to the reference data point than the target neighbor with index j (including a margin of safety).
getInsertions() - Static method in enum de.citec.tcs.alignment.comparators.OperationType
Returns an array containing the Insertion OperationTypes, namely INSERTION and SKIPINSERTION.
getJS() - Method in class de.citec.tcs.alignment.visualization.AbstractHTMLColumn
This default implementation returns an empty string.
getJS() - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
This method should return JavaScript containing code relevant for this column.
getK() - Method in class de.citec.tcs.alignment.learning.KNNClassifier
Returns the number of nearest neighbors that is considered by this classifier.
getK() - Method in class de.citec.tcs.alignment.learning.LMNNClassifier
Returns the number of considered nearest neighbors in the LMNN cost function.
getKeyword() - Method in class de.citec.tcs.alignment.comparators.AbstractValueComparatorWrapper
 
getKeyword() - Method in interface de.citec.tcs.alignment.comparators.ValueComparator
Returns the keyword for which values are compared by this ValueComparator.
getKeyword(int) - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
Returns the keyword for the given index.
getKeyword() - Method in class de.citec.tcs.alignment.sequence.KeywordSpecification
Returns the keyword.
getKeyword() - Method in class de.citec.tcs.alignment.visualization.AbstractHTMLColumn
 
getKeyword() - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
This method should return the keyword of this column.
getKeywordIndex(String) - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
Returns the index of the given keyword.
getKeywords() - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
Returns the keywords that are mapped.
getKeywords() - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
Returns a list of all keywords for which HTMLColumns exist within this HTMLVisualizer.
getKeywordSpecification(String) - Method in class de.citec.tcs.alignment.sequence.NodeSpecification
Returns the specification for the given keyword.
getKeywordSpecification(int) - Method in class de.citec.tcs.alignment.sequence.NodeSpecification
Returns the specification for the given keyword.
getKeywordSpecifications() - Method in class de.citec.tcs.alignment.sequence.NodeSpecification
 
getKNearest(int, int, double[]) - Static method in class de.citec.tcs.alignment.learning.DistanceIndex
Returns the indices of the K nearest neighbors of the reference data point sorted in ascending order with respect to their distance.
getKNearest(int, double[], DistanceIndex.IndexFilter) - Static method in class de.citec.tcs.alignment.learning.DistanceIndex
Returns the indices of the K data points with the lowest distance that meet some filter criterion.
getLabels() - Method in class de.citec.tcs.alignment.learning.AbstractDissimilarityClassifier
Returns the set of available class labels.
getLastAlignmentMatrix() - Method in class de.citec.tcs.alignment.AbstractStrictAlignmentAlgorithm
The last matrix that was calculated using this algorithm.
getLastDTWMatrix() - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
This returns the dynamic programming matrix that was calculated in the last call of calculateAlignment.
getLeft() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
 
getLeft() - Method in class de.citec.tcs.alignment.Alignment
 
getLeft() - Method in class de.citec.tcs.alignment.AlignmentList
 
getLeft() - Method in class de.citec.tcs.alignment.AlignmentMap
 
getLeft() - Method in class de.citec.tcs.alignment.CooptimalModel
 
getLeft() - Method in interface de.citec.tcs.alignment.DerivableAlignmentDistance
Returns the left sequence of this distance.
getLength() - Method in class de.citec.tcs.alignment.sequence.VectorialKeywordSpecification
The length all vectors for this keyword have to have.
getMargin() - Method in class de.citec.tcs.alignment.learning.LMNNClassifier
Returns the margin of safety that is required by the LMNN cost function.
getMax() - Method in class de.citec.tcs.alignment.comparators.AffineNormalizer
Returns the maximum possible value, which will be mapped to 1.
getMin() - Method in class de.citec.tcs.alignment.comparators.AffineNormalizer
Returns the minimum possible value, which will be mapped to 0.
getNodeSpecification() - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
getNodeSpecification() - Method in class de.citec.tcs.alignment.sequence.Sequence
Returns the NodeSpecification all Nodes in this sequence belong to.
getNonterminal() - Method in class de.citec.tcs.alignment.adp.ProductionRule
Returns the target nonterminal symbol of this rule.
getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
 
getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.DTWGrammar
 
getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
 
getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
 
getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
 
getNonterminalClass() - Method in interface de.citec.tcs.alignment.adp.Grammar
Returns the enum class that lists the nonterminal symbols of this grammar.
getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar
 
getNumberOfComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
 
getNumberOfComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
 
getNumberOfComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.ParameterLessComparisonBasedSkipExtendedComparator
 
getNumberOfComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.ParameterLessSkipExtendedComparator
 
getNumberOfComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
Implementing classes should return the number of (derivative-relevant) parameters used for the compare-function.
getNumberOfComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
 
getNumberOfParameters() - Method in class de.citec.tcs.alignment.comparators.AbstractDerivableValueComparatorWrapper
 
getNumberOfParameters() - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
getNumberOfParameters() - Method in interface de.citec.tcs.alignment.comparators.DerivableComparator
This shall return the number of parameters of this comparator.
getNumberOfParameters() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
getNumberOfParameters() - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
getNumColumns() - Method in class de.citec.tcs.alignment.visualization.AbstractHTMLColumn
 
getNumColumns() - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
This method should return the number of HTML columns occupied by this column.
getOperations() - Method in class de.citec.tcs.alignment.adp.ProductionRule
Returns the operations that are applied in this production rule.
getOriginalIndex(int) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
This is semantically equivalent to getNodeSpecification().getKeywordIndex(getKeyword(index)) but this is preprocessed here for better performance.
getParameters() - Method in class de.citec.tcs.alignment.comparators.AbstractDerivableValueComparatorWrapper
 
getParameters() - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
getParameters() - Method in interface de.citec.tcs.alignment.comparators.DerivableComparator
Return the current value of all parameters of this comparator.
getParameters() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
getParameters() - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
getPointsInRadius(double, double[], DistanceIndex.IndexFilter) - Static method in class de.citec.tcs.alignment.learning.DistanceIndex
Returns the indices of all data points, which have a lower distance than the given radius and meet some additional filter criterion.
getPossibleRules(AffineGrammar.Nonterminal, int, int, int, int) - Method in class de.citec.tcs.alignment.adp.AffineGrammar
 
getPossibleRules(DTWGrammar.Nonterminal, int, int, int, int) - Method in class de.citec.tcs.alignment.adp.DTWGrammar
 
getPossibleRules(N, int, int, int, int) - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
 
getPossibleRules(GlobalAsymmetricGrammar.Nonterminal, int, int, int, int) - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
 
getPossibleRules(GlobalGrammar.Nonterminal, int, int, int, int) - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
 
getPossibleRules(N, int, int, int, int) - Method in interface de.citec.tcs.alignment.adp.Grammar
Returns all production rules of this grammar that can be applied in the current situation.
getPossibleRules(SakoeChibaDTWGrammar.Nonterminal, int, int, int, int) - Method in class de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar
 
getProperty(String) - Static method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
 
getReplacements() - Static method in enum de.citec.tcs.alignment.comparators.OperationType
Returns an array containing the Replacement OperationTypes, namely REPLACEMENT, DELETIONREPLACEMENT and INSERTIONREPLACEMENT.
getResultClass() - Method in class de.citec.tcs.alignment.AbstractStrictAlignmentAlgorithm
 
getResultClass() - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
 
getResultClass() - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
 
getResultClass() - Method in class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm
 
getResultClass() - Method in interface de.citec.tcs.alignment.AlignmentAlgorithm
This method shall return the class of the alignment result.
getResultMatrix() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
Returns the results of the calculation as an object matrix.
getResults() - Method in class de.citec.tcs.alignment.parallel.Engine
Returns the results of this Engines last computation.
getRGBColor(double) - Static method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
Returns an hexadecimal rgb color string for the given score.
getRight() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
 
getRight() - Method in class de.citec.tcs.alignment.Alignment
 
getRight() - Method in class de.citec.tcs.alignment.AlignmentList
 
getRight() - Method in class de.citec.tcs.alignment.AlignmentMap
 
getRight() - Method in class de.citec.tcs.alignment.CooptimalModel
 
getRight() - Method in interface de.citec.tcs.alignment.DerivableAlignmentDistance
Returns the right sequence of this distance.
getRoundedString(double, int) - Static method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
Returns the string representation of the given number to the given precision.
getRules() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
Returns all production rules that are stored in this grammar.
getRuleSets() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar.RuleAvailabilityMatrix
 
getScores() - Method in class de.citec.tcs.alignment.AlignmentMap
Get all scores (sorted from low to high) for which Alignments exist within this map.
getSequence() - Method in class de.citec.tcs.alignment.sequence.Node
Returns the sequence this node belongs to.
getSize() - Method in class de.citec.tcs.alignment.AlignmentMap
Returns the number of Alignments stored in this map.
getSkips() - Static method in enum de.citec.tcs.alignment.comparators.OperationType
Returns an array containing the skip OperationTypes, namely SKIPDELETION and SKIPINSERTION.
getSourceCode(File, SourceCodeColumn.CodePosition, int) - Static method in class de.citec.tcs.alignment.visualization.SourceCodeColumn
Returns the source code located at the given CodePosition.
getSpecificationClass() - Method in enum de.citec.tcs.alignment.sequence.ValueType
Returns the corresponding specification class for this ValueType.
getSteps() - Method in class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
 
getSteps() - Method in interface de.citec.tcs.alignment.parallel.ProgressReporter
Returns the number of steps that already have been completed.
getString() - Method in class de.citec.tcs.alignment.sequence.StringValue
Returns the actual string.
getSymbol(int) - Method in class de.citec.tcs.alignment.sequence.Alphabet
This is equivalent to "getKeyword"
getSymbol() - Method in class de.citec.tcs.alignment.sequence.SymbolicValue
Returns this actual symbol.
getSymbolIndex(String) - Method in class de.citec.tcs.alignment.sequence.Alphabet
This is equivalent to "getKeywordIndex"
getSymbols() - Method in class de.citec.tcs.alignment.sequence.Alphabet
This is equivalent to "getKeywords"
getTabSize() - Method in class de.citec.tcs.alignment.visualization.NodeSourceCodeColumn
This manipulates as how many characters a tab should be counted.
getTabSize() - Method in interface de.citec.tcs.alignment.visualization.SourceCodeColumn.PositionExtractor
The tabulator size used in CodePositions returned by this PositionExtractor.
getTargetNeighborsTest(int, int, double[], int[]) - Static method in class de.citec.tcs.alignment.learning.DistanceIndex
Returns the indices of the K nearest neighbors of the reference data point that are from the same class as the reference data point.
getTargetNeighborsTraining(int, int, double[], int[]) - Static method in class de.citec.tcs.alignment.learning.DistanceIndex
Returns the indices of the K nearest neighbors of the reference data point that are from the same class as the reference data point.
getTargetNeighborsTraining(int, int, int, double[], int[]) - Static method in class de.citec.tcs.alignment.learning.DistanceIndex
Returns the indices of the K nearest neighbors of the reference data point that are from the same class as the reference data point.
getTotalSteps() - Method in interface de.citec.tcs.alignment.parallel.ProgressReporter
Returns the total number of steps that are necessary to complete the overall task.
getTrainingLabels() - Method in class de.citec.tcs.alignment.learning.AbstractDissimilarityClassifier
Returns the correct class labels for all given training data points.
getType() - Method in class de.citec.tcs.alignment.comparators.AbstractValueComparatorWrapper
 
getType() - Method in interface de.citec.tcs.alignment.comparators.ValueComparator
Returns the ValueType this comparator operates on.
getType() - Method in class de.citec.tcs.alignment.sequence.AbstractValue
 
getType() - Method in class de.citec.tcs.alignment.sequence.KeywordSpecification
Returns the specified type for that keyword.
getType() - Method in interface de.citec.tcs.alignment.sequence.Value
Returns the type of this value.
getValue(String) - Method in class de.citec.tcs.alignment.sequence.Node
Returns the value stored in this Node for the given keyword or null of no value is stored for the given keyword in this node.
getValue(int) - Method in class de.citec.tcs.alignment.sequence.Node
Returns the value stored in this Node for the given keyword or null of no value is stored for the given keyword in this node.
getValueClass() - Method in enum de.citec.tcs.alignment.sequence.ValueType
The corresponding class of this ValueType.
getVector() - Method in class de.citec.tcs.alignment.sequence.VectorialValue
Returns the actual vector.
getWeighting() - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
Returns the current keyword weighting.
GlobalAsymmetricGrammar - Class in de.citec.tcs.alignment.adp
This is a slight variation of the global alignment grammar.
GlobalAsymmetricGrammar() - Constructor for class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
Creates an instance of the global, asymmetric grammar.
GlobalAsymmetricGrammar.Nonterminal - Enum in de.citec.tcs.alignment.adp
 
GlobalGrammar - Class in de.citec.tcs.alignment.adp
This is the most basic (and classic) alignment grammar there is.
GlobalGrammar() - Constructor for class de.citec.tcs.alignment.adp.GlobalGrammar
This creates an instance of the global alignment grammar.
GlobalGrammar.Nonterminal - Enum in de.citec.tcs.alignment.adp
 
Gradient - Interface in de.citec.tcs.alignment.comparators
An interface to support sparse gradients.
Grammar<N extends Enum<N>> - Interface in de.citec.tcs.alignment.adp
An Algebraic Dynamic Programming (ADP) grammar is a regular tree grammar.
GrammarValidityException - Exception in de.citec.tcs.alignment.adp
This exception is thrown if a flexible grammar is invalid.
GrammarValidityException(String) - Constructor for exception de.citec.tcs.alignment.adp.GrammarValidityException
 

H

hasCoherentReplacementCost() - Method in class de.citec.tcs.alignment.comparators.AbstractValueComparatorWrapper
 
hasCoherentReplacementCost() - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
hasCoherentReplacementCost() - Method in interface de.citec.tcs.alignment.comparators.Comparator
This method should return true if and only if this Comparator guarantees that compare(OperationType.REPLACEMENT, x, y) = compare(OperationType.DELETIONREPLACEMENT, x, y) = compare(OperationType.INSERTIONREPLACEMENT, x, y) for all possible inputs x, y.
hasCoherentReplacementCost() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
hasCoherentReplacementCost() - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
hashCode() - Method in class de.citec.tcs.alignment.adp.DPCellId
 
hashCode() - Method in class de.citec.tcs.alignment.adp.ProductionRule
 
hashCode() - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
hashCode() - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
hashCode() - Method in class de.citec.tcs.alignment.comparators.EuclideanComparator
 
hashCode() - Method in class de.citec.tcs.alignment.comparators.ExponentialNormalizer
 
hashCode() - Method in class de.citec.tcs.alignment.comparators.HyperbolicNormalizer
 
hashCode() - Method in class de.citec.tcs.alignment.comparators.L1NormComparator
 
hashCode() - Method in class de.citec.tcs.alignment.comparators.NCDComparator
 
hashCode() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
hashCode() - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
hashCode() - Method in class de.citec.tcs.alignment.learning.DistanceIndex
 
hashCode() - Method in class de.citec.tcs.alignment.Operation
 
hashCode() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine.MatrixCoordinate
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.AbstractValue
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.KeywordSpecification
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.Node
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.NodeSpecification
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.Sequence
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.StringValue
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.SymbolicValue
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.VectorialKeywordSpecification
 
hashCode() - Method in class de.citec.tcs.alignment.sequence.VectorialValue
 
hasKeyword(String) - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
Returns true if and only if this keyword is contained in the mapping.
hasSymbol(String) - Method in class de.citec.tcs.alignment.sequence.Alphabet
This is equivalent to "hasKeyword".
highestScore() - Method in class de.citec.tcs.alignment.AlignmentMap
Returns the highest/worst score stored in this map.
HTMLColumn<X,Y> - Interface in de.citec.tcs.alignment.visualization
This is an interface for classes that provide additional information for the HTML output in form of columns in the HTML table.
HTMLVisualizer<X,Y> - Class in de.citec.tcs.alignment.visualization
This creates an HTML table visualization of an Alignment.
HTMLVisualizer() - Constructor for class de.citec.tcs.alignment.visualization.HTMLVisualizer
 
HyperbolicNormalizer - Class in de.citec.tcs.alignment.comparators
This normalizes by using the function 1 - 1/(alpha*d+1).
HyperbolicNormalizer() - Constructor for class de.citec.tcs.alignment.comparators.HyperbolicNormalizer
 

I

i - Variable in class de.citec.tcs.alignment.adp.DPCellId
 
i - Variable in class de.citec.tcs.alignment.parallel.MatrixEngine.MatrixCoordinate
 
ident - Variable in class de.citec.tcs.alignment.parallel.Engine.CalculationResult
 
IdentityNormalizer - Class in de.citec.tcs.alignment.comparators
A normalizer implementing just the identity function
IdentityNormalizer() - Constructor for class de.citec.tcs.alignment.comparators.IdentityNormalizer
 
importNodeSpecification(String) - Static method in class de.citec.tcs.alignment.csv.CSVImporter
This imports a NodeSpecification from a JSON file.
importNodeSpecification(File) - Static method in class de.citec.tcs.alignment.csv.CSVImporter
This imports a NodeSpecification from a JSON file.
importNodeSpecification(Reader) - Static method in class de.citec.tcs.alignment.csv.CSVImporter
This imports a NodeSpecification from a Reader.
importSequence(NodeSpecification, String) - Static method in class de.citec.tcs.alignment.csv.CSVImporter
This imports a sequence from a CSV file using the default delimiter "\t".
importSequence(NodeSpecification, File) - Static method in class de.citec.tcs.alignment.csv.CSVImporter
This imports a sequence from a CSV file using the default delimiter "\t".
importSequence(NodeSpecification, Reader) - Static method in class de.citec.tcs.alignment.csv.CSVImporter
This imports a sequence from a Reader using the default delimiter "\t".
importSequence(NodeSpecification, String, String) - Static method in class de.citec.tcs.alignment.csv.CSVImporter
This imports a sequence from a CSV file using the given delimiter string.
importSequence(NodeSpecification, File, String) - Static method in class de.citec.tcs.alignment.csv.CSVImporter
This imports a sequence from a CSV file using the given delimiter string.
importSequence(NodeSpecification, Reader, String) - Static method in class de.citec.tcs.alignment.csv.CSVImporter
This imports a sequence from a Reader containing CSV data using the given delimiter string.
incrementSteps() - Method in class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
 
incrementSteps() - Method in interface de.citec.tcs.alignment.parallel.ProgressReporter
Notes that one additional step has been completed.
index(String) - Method in class de.citec.tcs.alignment.comparators.IndexingAlphabetWrapper
 
index(X) - Method in interface de.citec.tcs.alignment.comparators.IndexingFunction
This function maps the given object to its index.
index - Variable in class de.citec.tcs.alignment.learning.DistanceIndex
 
IndexingAlphabetWrapper - Class in de.citec.tcs.alignment.comparators
A wrapper for an Alphabet to make it compatible with the IndexingFunction interface.
IndexingAlphabetWrapper(Alphabet) - Constructor for class de.citec.tcs.alignment.comparators.IndexingAlphabetWrapper
 
IndexingFunction<X> - Interface in de.citec.tcs.alignment.comparators
An indexing function maps a value from a finite set to its index.
IndexingScheme - Class in de.citec.tcs.alignment.sequence
This serves as an abstract superclass for classes that define an indexing scheme for keywords.
IndexingScheme(IndexingScheme) - Constructor for class de.citec.tcs.alignment.sequence.IndexingScheme
This performs a shallow copy of the given other IndexingScheme, meaning that only references are copied and manipulations of the given other IndexingScheme will influence the copy as well.
IndexingScheme(HashMap<String, Integer>) - Constructor for class de.citec.tcs.alignment.sequence.IndexingScheme
Constructs an IndexingScheme from a mapping of strings to indices.
IndexingScheme(String[]) - Constructor for class de.citec.tcs.alignment.sequence.IndexingScheme
Constructs an IndexingScheme from a mapping of indices to strings.
IndexingScheme(String) - Constructor for class de.citec.tcs.alignment.sequence.IndexingScheme
Constructor for symbols either encoded as single characters without delimiter or as strings with | as delimiter.
isEndExclusive() - Method in class de.citec.tcs.alignment.visualization.NodeSourceCodeColumn
Sets if the end column of each given codePosition should be in- or excluded in the visualization.
isValid(Grammar, Comparator) - Static method in class de.citec.tcs.alignment.adp.ComparatorValidator
Returns true if and only if the given Comparator supports all OperationType the given Grammar requires.
isValid(AlignmentAlgorithm<X, Y, ?>, Comparator<? extends X, ? extends Y>) - Static method in class de.citec.tcs.alignment.ComparatorValidator
Returns true if and only if the given Comparator supports all OperationType the given AlignmentAlgorithm requires.
isValidWeighting(double[]) - Static method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
This checks whether the given weighting is a valid one.
isValidWeighting(double[]) - Static method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
This checks whether the given weighting is a valid one.

J

j - Variable in class de.citec.tcs.alignment.adp.DPCellId
 
j - Variable in class de.citec.tcs.alignment.parallel.MatrixEngine.MatrixCoordinate
 

K

KeywordSpecification - Class in de.citec.tcs.alignment.sequence
This specifies a keyword via its name and the type of its values.
KeywordSpecification(String, ValueType) - Constructor for class de.citec.tcs.alignment.sequence.KeywordSpecification
Sets up a KeywordSpecification that defines a type for the given keyword.
KNNClassifier - Class in de.citec.tcs.alignment.learning
This implements a very basic k-nearest neighbor classifier: Given a set of data points and a (trained) AlignmentAlgorithm it can determine the k next datapoints for a given new datapoint and calculate the label for it based on the majority of votes.
KNNClassifier(int[]) - Constructor for class de.citec.tcs.alignment.learning.KNNClassifier
 

L

L1NormComparator - Class in de.citec.tcs.alignment.comparators
Compares vectors using the L1-Norm.
L1NormComparator(int) - Constructor for class de.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(Normalizer, int) - Constructor for class de.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(int, double) - Constructor for class de.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(Normalizer, int, double) - Constructor for class de.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(double[], double[], double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(Normalizer, double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(Normalizer, double[], double[], double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.L1NormComparator
 
labels - Variable in class de.citec.tcs.alignment.learning.DistanceIndex.Labelfilter
 
left - Variable in class de.citec.tcs.alignment.learning.DistanceIndex.AndFilter
 
LinearNormalizer - Class in de.citec.tcs.alignment.comparators
A normalizer that just multiplies the input value by a constant, such that the given maximum is mapped to 1.
LinearNormalizer(double) - Constructor for class de.citec.tcs.alignment.comparators.LinearNormalizer
 
ListGradient - Class in de.citec.tcs.alignment.comparators
A list-based implementation of the Gradient interface.
ListGradient() - Constructor for class de.citec.tcs.alignment.comparators.ListGradient
 
LMNNClassifier - Class in de.citec.tcs.alignment.learning
This implements a Large Margin Nearest Neighbor classifier as suggested by Weinberger, Saul et al.
LMNNClassifier(int[]) - Constructor for class de.citec.tcs.alignment.learning.LMNNClassifier
 
LMNNGradientCalculator<X> - Class in de.citec.tcs.alignment.learning
This implements the Large Margin Nearest Neighbor Metric Learning approach by Weinberger et al.
LMNNGradientCalculator(List<? extends List<X>>, int[], AlignmentAlgorithm<X, X, ? extends DerivableAlignmentDistance<X, X>>) - Constructor for class de.citec.tcs.alignment.learning.LMNNGradientCalculator
 
lowestScore() - Method in class de.citec.tcs.alignment.AlignmentMap
Returns the lowest/best score stored in this map.

M

mapToDoubleVector(Object) - Static method in class de.citec.tcs.alignment.sequence.VectorialValue
Tries to convert an object to a double vector.
MatrixEngine<R> - Class in de.citec.tcs.alignment.parallel
This is a subclass of the Engine class to enable parallel processing to calculate the entries of a matrix.
MatrixEngine(int, int, Class<R>) - Constructor for class de.citec.tcs.alignment.parallel.MatrixEngine
 
MatrixEngine.MatrixCoordinate - Class in de.citec.tcs.alignment.parallel
This identifies a coordinate in a matrix as a tuple of row index and column index.
MatrixEngine.MatrixCoordinate(int, int) - Constructor for class de.citec.tcs.alignment.parallel.MatrixEngine.MatrixCoordinate
 
META_COLUMN_IDS - Static variable in class de.citec.tcs.alignment.visualization.HTMLVisualizer
 

N

NCDComparator - Class in de.citec.tcs.alignment.comparators
This compares strings using normalized compression distance.
NCDComparator() - Constructor for class de.citec.tcs.alignment.comparators.NCDComparator
 
NCDComparator.CompressorType - Enum in de.citec.tcs.alignment.comparators
This class contains all possible CompressorTypes for this NCD implementation.
next() - Method in class de.citec.tcs.alignment.comparators.ArrayGradient
 
next() - Method in class de.citec.tcs.alignment.comparators.EmptyGradient
 
next() - Method in interface de.citec.tcs.alignment.comparators.Gradient
Iterates to the next gradient value.
next() - Method in class de.citec.tcs.alignment.comparators.ListGradient
 
next() - Method in class de.citec.tcs.alignment.comparators.SingletonGradient
 
Node - Class in de.citec.tcs.alignment.sequence
This is a node in a Sequence storing values for the keywords defined in the sequence.
Node(Sequence) - Constructor for class de.citec.tcs.alignment.sequence.Node
 
NodeSourceCodeColumn - Class in de.citec.tcs.alignment.visualization
This special HTML column allows users to visualize source code, given that you have put the information on the location into the Sequence, meaning that your NodeSpecification has two keywords, one specifying the path to the respective code file and one specifying the position within that code file.
NodeSourceCodeColumn(String, String, String) - Constructor for class de.citec.tcs.alignment.visualization.NodeSourceCodeColumn
 
NodeSourceCodeColumn(String, String, String, int) - Constructor for class de.citec.tcs.alignment.visualization.NodeSourceCodeColumn
 
NodeSourceCodeColumn(String, String, File, String) - Constructor for class de.citec.tcs.alignment.visualization.NodeSourceCodeColumn
 
NodeSourceCodeColumn(String, String, File, String, int) - Constructor for class de.citec.tcs.alignment.visualization.NodeSourceCodeColumn
 
NodeSpecification - Class in de.citec.tcs.alignment.sequence
This specifies the contents of the nodes in a given sequence.
NodeSpecification(KeywordSpecification[]) - Constructor for class de.citec.tcs.alignment.sequence.NodeSpecification
 
norm(double[]) - Static method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanComparator
Calculates the L2 norm/Euclidean norm of the given input vector.
norm(double[], double[]) - Static method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
Calculates the relevance-weighted L2 norm/Euclidean norm of the given input vector.
norm(double[]) - Static method in class de.citec.tcs.alignment.comparators.NormalizedL1Comparator
Calculates the L1 norm/Manhattan norm of the given input vector.
norm(double[], double[]) - Static method in class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
Calculates the relevance-weighted L1 norm of the given input vector.
normalize(double) - Method in class de.citec.tcs.alignment.comparators.AffineNormalizer
 
normalize(double) - Method in class de.citec.tcs.alignment.comparators.ExponentialNormalizer
 
normalize(double) - Method in class de.citec.tcs.alignment.comparators.HyperbolicNormalizer
 
normalize(double) - Method in class de.citec.tcs.alignment.comparators.IdentityNormalizer
 
normalize(double) - Method in class de.citec.tcs.alignment.comparators.LinearNormalizer
 
normalize(double) - Method in interface de.citec.tcs.alignment.comparators.Normalizer
 
NormalizedEuclideanComparator - Class in de.citec.tcs.alignment.comparators
Implements a normalized L2 distance, defined as: ||x - y|| / (||x|| + ||y||) .
NormalizedEuclideanComparator(int) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedEuclideanComparator
 
NormalizedEuclideanComparator(int, double) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedEuclideanComparator
 
NormalizedEuclideanComparator(double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedEuclideanComparator
 
NormalizedEuclideanComparator(double[], double[], double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedEuclideanComparator
 
NormalizedEuclideanRelevanceComparator - Class in de.citec.tcs.alignment.comparators
Implements a normalized relevance L2 distance, defined as: ||Λ * x - Λ * y|| / (||Λ * x|| + ||Λ * y||) where Λ is a diagonal matrix.
NormalizedEuclideanRelevanceComparator(int) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
 
NormalizedEuclideanRelevanceComparator(int, double) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
 
NormalizedEuclideanRelevanceComparator(double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
 
NormalizedEuclideanRelevanceComparator(double[], double[], double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
 
normalizeDissimilarity(double, List<X>, List<Y>) - Static method in class de.citec.tcs.alignment.AbstractStrictAlignmentAlgorithm
Normalizes the given raw distance by the worst case that could occur in an alignment of the two sequences: In the worst case, we replace all elements in a with elements in b and delete/insert the remaining elements in the longer sequence.
normalizeDissimilarity(double, List<X>, List<Y>) - Static method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
Normalizes the given raw distance by the worst case that could occur in an alignment of the two sequences: In the worst case, we replace all elements in a with elements in b and delete-replace/insert-replace the remaining elements in the longer sequence.
normalizeDissimilarity(double, List<X>, List<Y>) - Static method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
Normalizes the given raw distance by the worst case that could occur in an alignment of the two sequences: In the worst case, we replace all elements in a with elements in b and delete/insert the remaining elements in the longer sequence.
normalizeDissimilarity(double, List<X>, List<Y>) - Static method in class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm
Normalizes the given raw distance by the worst case that could occur in an alignment of the two sequences: In the worst case, we replace all elements in a with elements in b and delete/insert the remaining elements in the longer sequence.
NormalizedL1Comparator - Class in de.citec.tcs.alignment.comparators
Implements a normalized L1 distance, defined as: |x - y| / (|x| + |y|) .
NormalizedL1Comparator(int) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedL1Comparator
 
NormalizedL1Comparator(int, double) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedL1Comparator
 
NormalizedL1Comparator(double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedL1Comparator
 
NormalizedL1Comparator(double[], double[], double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedL1Comparator
 
NormalizedL1RelevanceComparator - Class in de.citec.tcs.alignment.comparators
Implements a normalized relevance L1 distance, defined as: |Λ * x - Λ * y| / (|Λ * x| + |Λ * y|) where Λ is a diagonal matrix.
NormalizedL1RelevanceComparator(int) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
 
NormalizedL1RelevanceComparator(int, double) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
 
NormalizedL1RelevanceComparator(double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
 
NormalizedL1RelevanceComparator(double[], double[], double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
 
Normalizer - Interface in de.citec.tcs.alignment.comparators
A Normalizer specifies a function to normalize arbitrary distance values between 0 and infinity to the realm of 0 to 1.
notEmpty() - Method in class de.citec.tcs.alignment.comparators.ArrayGradient
 
notEmpty() - Method in class de.citec.tcs.alignment.comparators.EmptyGradient
 
notEmpty() - Method in interface de.citec.tcs.alignment.comparators.Gradient
Returns true if and only if the current entry exists, that is, the entries are not yet all consumed.
notEmpty() - Method in class de.citec.tcs.alignment.comparators.ListGradient
 
notEmpty() - Method in class de.citec.tcs.alignment.comparators.SingletonGradient
 

O

Operation<X,Y> - Class in de.citec.tcs.alignment
This defines an applied Alignment Operation.
Operation(X, Y, OperationType, double) - Constructor for class de.citec.tcs.alignment.Operation
This constructs an Operation within an AlignmentPath.
Operation(Operation<X, Y>) - Constructor for class de.citec.tcs.alignment.Operation
A copy constructor.
OperationType - Enum in de.citec.tcs.alignment.comparators
This defines the possible types of operations that may be used in an alignment within this Toolbox.
ordinal - Variable in class de.citec.tcs.alignment.adp.DPCellId
 

P

ParallelGradientEngine<X,Y> - Class in de.citec.tcs.alignment
This allows parallel processing of gradient calculations.
ParallelGradientEngine(Map<MatrixEngine.MatrixCoordinate, DerivableAlignmentDistance<X, Y>>, int, int, DerivableComparator<X, Y>) - Constructor for class de.citec.tcs.alignment.ParallelGradientEngine
Creates a ParallelGradientEngine that computes gradients for several DeriableAlignmentDistance objects in parallel.
ParallelGradientEngine(Collection<Engine.CalculationResult<? extends MatrixEngine.MatrixCoordinate, ? extends DerivableAlignmentDistance<X, Y>>>, int, int, DerivableComparator<X, Y>) - Constructor for class de.citec.tcs.alignment.ParallelGradientEngine
Creates a ParallelGradientEngine that computes gradients for several DeriableAlignmentDistance objects in parallel.
ParallelGradientEngine(DerivableAlignmentDistance<X, Y>[][], DerivableComparator<X, Y>) - Constructor for class de.citec.tcs.alignment.ParallelGradientEngine
Creates a ParallelGradientEngine that computes gradients for several DeriableAlignmentDistance objects in parallel.
ParallelProcessingEngine<X,Y,R> - Class in de.citec.tcs.alignment
This allows parallel processing of alignment calculations.
ParallelProcessingEngine(AlignmentAlgorithm<X, Y, R>, List<? extends List<X>>, List<? extends List<Y>>) - Constructor for class de.citec.tcs.alignment.ParallelProcessingEngine
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm and the given Sequences.
ParameterLessComparisonBasedSkipExtendedComparator<X,Y> - Class in de.citec.tcs.alignment.comparators
A convenience implementation for ComparisonBasedSkipExtendedComparators without (own) parameters.
ParameterLessComparisonBasedSkipExtendedComparator(Y, X, Y, X) - Constructor for class de.citec.tcs.alignment.comparators.ParameterLessComparisonBasedSkipExtendedComparator
 
ParameterLessComparisonBasedSkipExtendedComparator(Y, X) - Constructor for class de.citec.tcs.alignment.comparators.ParameterLessComparisonBasedSkipExtendedComparator
 
ParameterLessSkipExtendedComparator<X,Y> - Class in de.citec.tcs.alignment.comparators
A convenience implementation for SkipExtendedComparators without (own) parameters.
ParameterLessSkipExtendedComparator() - Constructor for class de.citec.tcs.alignment.comparators.ParameterLessSkipExtendedComparator
 
path - Variable in class de.citec.tcs.alignment.visualization.SourceCodeColumn.CodePosition
 
ProductionRule<N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
A ProductionRule actually represents the right hand side of a production rule in an ADP grammar.
ProductionRule(OperationType[], N) - Constructor for class de.citec.tcs.alignment.adp.ProductionRule
Creates a new production rule of the form A → operation_1( ...
ProductionRule(OperationType, N) - Constructor for class de.citec.tcs.alignment.adp.ProductionRule
Creates a new production rule of the form A → operation(left, B, right)
ProductionRule(N) - Constructor for class de.citec.tcs.alignment.adp.ProductionRule
Creats a new production rule of the form A → B Use these rules with care as they may produce endless loops if you put them in a cycle, like A → B → C → ...
ProgressReporter - Interface in de.citec.tcs.alignment.parallel
This is an interface for classes that measure (and report) the progress of a task with a discrete number of steps.
put(Alignment<X, Y>) - Method in class de.citec.tcs.alignment.AlignmentMap
Adds a new Alignment to this map.

R

RandomSequenceGenerator - Class in de.citec.tcs.alignment.wrappers
This class is more for demonstration purposes and creates random sequences according to given input parameters.
RandomSequenceGenerator() - Constructor for class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
 
range() - Method in class de.citec.tcs.alignment.comparators.IndexingAlphabetWrapper
 
range() - Method in interface de.citec.tcs.alignment.comparators.IndexingFunction
The number of indices used by this index.
referenceIndex - Variable in class de.citec.tcs.alignment.learning.DistanceIndex.IdentityFilter
 
referenceLabel - Variable in class de.citec.tcs.alignment.learning.DistanceIndex.Labelfilter
 
removeAlignments(double) - Method in class de.citec.tcs.alignment.AlignmentMap
Removes all Alignments with the given score from the map and returns them.
removeDiagonal() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
Ensures that the diagonal of the matrix is not calculated at the next call to "calculate".
removeTask(I) - Method in class de.citec.tcs.alignment.parallel.Engine
Removes the task with the given identifier from this Engine.
removeTasks(I[]) - Method in class de.citec.tcs.alignment.parallel.Engine
Removes the tasks with the given identifiers from this Engine.
removeTasks(Collection<I>) - Method in class de.citec.tcs.alignment.parallel.Engine
Removes the tasks with the given identifiers from this Engine.
requires(OperationType) - Method in class de.citec.tcs.alignment.AbstractStrictAlignmentAlgorithm
 
requires(OperationType) - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
 
requires(OperationType) - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
 
requires(OperationType) - Method in class de.citec.tcs.alignment.adp.AffineGrammar
 
requires(OperationType) - Method in class de.citec.tcs.alignment.adp.DTWGrammar
 
requires(OperationType) - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
 
requires(OperationType) - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
 
requires(OperationType) - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
 
requires(OperationType) - Method in interface de.citec.tcs.alignment.adp.Grammar
This method should return true if and only if this Grammar uses the given OperationType.
requires(OperationType) - Method in class de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar
 
requires(OperationType) - Method in class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm
 
requires(OperationType) - Method in interface de.citec.tcs.alignment.AlignmentAlgorithm
This method should return true if and only if this AlignmentAlgorithm uses the given operation.
resetSteps() - Method in class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
 
resetSteps() - Method in interface de.citec.tcs.alignment.parallel.ProgressReporter
Resets the number of completed steps to zero.
result - Variable in class de.citec.tcs.alignment.parallel.Engine.CalculationResult
 
right - Variable in class de.citec.tcs.alignment.learning.DistanceIndex.AndFilter
 

S

SakoeChibaDTWGrammar - Class in de.citec.tcs.alignment.adp
This is a grammar for dynamic time warping.
SakoeChibaDTWGrammar() - Constructor for class de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar
 
SakoeChibaDTWGrammar.Nonterminal - Enum in de.citec.tcs.alignment.adp
 
Sequence - Class in de.citec.tcs.alignment.sequence
Usually a sequence for alignments is defined as a sequence of symbols.
Sequence(NodeSpecification) - Constructor for class de.citec.tcs.alignment.sequence.Sequence
Sets up an empty sequence with the given NodeSpecification as basis.
Sequence(String) - Constructor for class de.citec.tcs.alignment.sequence.Sequence
Sets up a trivial sequence with only one keyword (DEFAULTKEYWORD) and treats the string content between | delimiters in the input string as symbolic values.
Sequence(String, Alphabet) - Constructor for class de.citec.tcs.alignment.sequence.Sequence
Sets up a trivial sequence with only one keyword (DEFAULTKEYWORD) and treats the string content between | delimiters in the input string as symbolic values.
setAlpha(double) - Method in class de.citec.tcs.alignment.comparators.HyperbolicNormalizer
 
setBandWidth(int) - Method in class de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar
Sets the Sakoe-Chiba bandwidth.
setBeta(double) - Method in class de.citec.tcs.alignment.comparators.ExponentialNormalizer
 
setComparator(Comparator<X, Y>) - Method in class de.citec.tcs.alignment.AbstractStrictAlignmentAlgorithm
 
setComparator(Comparator<X, Y>) - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
 
setComparator(Comparator<X, Y>) - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
 
setComparator(Comparator<X, Y>) - Method in class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm
 
setComparator(Comparator<X, Y>) - Method in interface de.citec.tcs.alignment.AlignmentAlgorithm
This should set the Comparator used to compute local distances for this algorithm.
setComparator(String, ValueComparator) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
Sets the comparator for a given keyword.
setComparator(int, ValueComparator) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
Sets the comparator for a given keyword.
setComparisonParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
 
setComparisonParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
 
setComparisonParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.ParameterLessComparisonBasedSkipExtendedComparator
 
setComparisonParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.ParameterLessSkipExtendedComparator
 
setComparisonParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
Sets the current value of all parameters of this comparator.
setComparisonParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
 
setEndExclusive(boolean) - Method in class de.citec.tcs.alignment.visualization.NodeSourceCodeColumn
Sets if the end column of each given codePosition should be in- or excluded in the visualization.
setFull() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
Clears all current calculation tasks and instead adds a task for every matrix entry, such that the full matrix is calculated on the next call of the "calculate" method.
setFull() - Method in class de.citec.tcs.alignment.ParallelGradientEngine
Overrides the setFull() method of matrix engine.
setK(int) - Method in class de.citec.tcs.alignment.learning.KNNClassifier
Sets the number of nearest neighbors that is considered by this classifier.
setK(int) - Method in class de.citec.tcs.alignment.learning.LMNNClassifier
Sets the number of considered nearest neighbors in the LMNN cost function.
setMargin(double) - Method in class de.citec.tcs.alignment.learning.LMNNClassifier
Sets the margin of safety that is required by the LMNN cost function.
setMax(double) - Method in class de.citec.tcs.alignment.comparators.AffineNormalizer
Sets the maximum possible value, which will be mapped to 1.
setMin(double) - Method in class de.citec.tcs.alignment.comparators.AffineNormalizer
Sets the minimum possible value, which will be mapped to 0.
setParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.AbstractDerivableValueComparatorWrapper
 
setParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
setParameters(double[]) - Method in interface de.citec.tcs.alignment.comparators.DerivableComparator
Sets the current value of all parameters of this comparator.
setParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
setParameters(double[]) - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
setPathLimit(int) - Method in class de.citec.tcs.alignment.StrictAlignmentAllOptimalAlgorithm
The total number of co-optimal alignments can be very huge as multiple co-optimal operations lead to a combinatorial explosion of possible alignments.
setRelevanceWeights(double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedEuclideanRelevanceComparator
The vector of relevance weights for each dimension.
setRelevanceWeights(double[]) - Method in class de.citec.tcs.alignment.comparators.NormalizedL1RelevanceComparator
The vector of relevance weights for each dimension.
setReplacementMatrix(double[][]) - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
setSpecificTasks(boolean[][]) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
Clears all current calculation tasks and instead adds a task for every matrix entry that is set to "true" in the given boolean matrix.
setSpecificTasks(MatrixEngine.MatrixCoordinate[]) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
Clears all current calculation tasks and instead adds a task for every given matrix coordinate.
setSpecificTasks(Collection<MatrixEngine.MatrixCoordinate>) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
Clears all current calculation tasks and instead adds a task for every given matrix coordinate.
setSpecificTasks(int[][]) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
Clears all current calculation tasks and instead adds a task for every given matrix coordinate.
setString(String) - Method in class de.citec.tcs.alignment.sequence.StringValue
 
setSymbol(String) - Method in class de.citec.tcs.alignment.sequence.SymbolicValue
Sets the actual symbol.
setSymmetric() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
Clears all current calculation tasks and instead adds a task for every matrix entry in the upper half of the matrix.
setTabSize(int) - Method in class de.citec.tcs.alignment.visualization.NodeSourceCodeColumn
This manipulates as how many characters a tab should be counted.
setTotalSteps(int) - Method in interface de.citec.tcs.alignment.parallel.ProgressReporter
Sets the total number of steps that are necessary to complete the overall task.
setUpSpecification(Sequence[]) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
Sets up a default AlignmentSpecification for the simple StringEditDistance problem.
setUpSpecification(Sequence[], double, double, double, double) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
Sets up an AlignmentSpecification for the simple StringEditDistance problem.
setUpSpecification(Sequence[], double[][]) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
Sets up an AlignmentSpecification for the simple StringEditDistance problem.
setUpSpecification(Sequence[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], ValueComparator) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], ValueComparator[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], double[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], ValueComparator, double[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], ValueComparator[], double[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setValue(String, Value) - Method in class de.citec.tcs.alignment.sequence.Node
Sets the value for the given keyword.
setValue(int, Value) - Method in class de.citec.tcs.alignment.sequence.Node
Sets the value for the given keyword.
setVector(double[]) - Method in class de.citec.tcs.alignment.sequence.VectorialValue
Sets the actual vector.
setVector(Object) - Method in class de.citec.tcs.alignment.sequence.VectorialValue
Sets the actual vector.
setWeighting(double[]) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
This sets the current weighting of keywords.
SingletonGradient - Class in de.citec.tcs.alignment.comparators
A Gradient with a single entry.
SingletonGradient(int, double) - Constructor for class de.citec.tcs.alignment.comparators.SingletonGradient
 
size() - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
Returns the number of mapped keywords.
SkipExtendedComparator<X,Y> - Class in de.citec.tcs.alignment.comparators
This is an abstract class to be used for Comparators that are only to be used for comparisons per se but can be extended for use with gaps and skips.
SkipExtendedComparator() - Constructor for class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
smartObjectToString(Object) - Static method in class de.citec.tcs.alignment.visualization.VisualizerUtils
This toString method checks whether the input is an array and returns the according string representation.
SoftADPFullAlgorithm<X,Y,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This algorithm returns a SoftADPPathModel based on the given grammar and algebra/AlignmentSpecification.
SoftADPFullAlgorithm(Grammar<N>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.adp.SoftADPFullAlgorithm
Creates a new SoftFullAlgorithm based on the given ADP grammar and the given Comparator/algebra.
SoftADPPathModel<X,Y,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This is basically a large storage class for all results of a SoftADPFullAlgorithm to facilitate derivative calculation.
SoftADPPathModel(Comparator<X, Y>, Grammar<N>, double, double, double, EnumMap<N, double[][]>, EnumMap<OperationType, double[][]>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Constructor for class de.citec.tcs.alignment.adp.SoftADPPathModel
 
SoftADPScoreAlgorithm<X,Y,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This algorithm calculates the soft alignment score for the given input grammar and algebra/AlignmentSpecification.
SoftADPScoreAlgorithm(Grammar<N>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.adp.SoftADPScoreAlgorithm
 
Softmin - Class in de.citec.tcs.alignment
This implements utility functions for the softmin function.
Softmin() - Constructor for class de.citec.tcs.alignment.Softmin
 
softmin(double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
This calculates softmin for the given input and the given value of beta.
softmin(double, double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
This calculates softmin for the given input and the given value of beta.
SourceCodeColumn<X,Y> - Class in de.citec.tcs.alignment.visualization
This special HTML column allows users to visualize source code corresponding to the elements in the input sequences, given that the location of the source code snippet can be extracted from input elements.
SourceCodeColumn(SourceCodeColumn.PositionExtractor<X>, SourceCodeColumn.PositionExtractor<Y>, String) - Constructor for class de.citec.tcs.alignment.visualization.SourceCodeColumn
 
SourceCodeColumn(SourceCodeColumn.PositionExtractor<X>, SourceCodeColumn.PositionExtractor<Y>, File, String, int) - Constructor for class de.citec.tcs.alignment.visualization.SourceCodeColumn
 
SourceCodeColumn.CodePosition - Class in de.citec.tcs.alignment.visualization
A simple class that is meant to store an interval in source code, starting at a certain line and column and ending at a certain line and column.
SourceCodeColumn.CodePosition(String, int, int, int, int) - Constructor for class de.citec.tcs.alignment.visualization.SourceCodeColumn.CodePosition
 
SourceCodeColumn.PositionExtractor<X> - Interface in de.citec.tcs.alignment.visualization
An interface for functions that extract a CodePosition from an object.
SparseAbstractADPAlgorithm<X,Y,R,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This is the most abstract ADP algorithm just implementing the forward calculation of the dynamic programming tables for an arbitrary sparse grammar.
SparseAbstractADPAlgorithm(SparseGrammar<N>, Class<R>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm
 
SparseAbstractADPAlgorithm.SparseMatrix - Class in de.citec.tcs.alignment.adp
This is the SparseMatrix class we use within this algorithm.
SparseAbstractADPAlgorithm.SparseMatrix() - Constructor for class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm.SparseMatrix
 
SparseGrammar<N extends Enum<N>> - Interface in de.citec.tcs.alignment.adp
This is a special kind of ADP grammar, that limits the dynamic programming matrix to a few cells and thus supports a sparse dynamic programming matrix, which (ideally) reduces the runtime to linear time.
SparseStrictADPFullAlgorithm<X,Y,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This algorithm calculates an optimal AlignmentPath using the given ADP grammar and algebra/AlignmentSpecification.
SparseStrictADPFullAlgorithm(SparseGrammar<N>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.adp.SparseStrictADPFullAlgorithm
 
SparseStrictADPScoreAlgorithm<X,Y,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This algorithm calculates the strict alignment score for the given input grammar and algebra/AlignmentSpecification.
SparseStrictADPScoreAlgorithm(SparseGrammar<N>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.adp.SparseStrictADPScoreAlgorithm
 
SquareParallelProcessingEngine<X,R> - Class in de.citec.tcs.alignment
This allows parallel processing of alignment calculations.
SquareParallelProcessingEngine(AlignmentAlgorithm<X, X, R>, List<? extends List<X>>) - Constructor for class de.citec.tcs.alignment.SquareParallelProcessingEngine
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm and the given Sequences.
SquareReplacementMatrixComparator<X> - Class in de.citec.tcs.alignment.comparators
This comparator defines explicit replacement (and deletion/insertion) costs for comparison of values from a discrete set.
SquareReplacementMatrixComparator(IndexingFunction<X>) - Constructor for class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
SquareReplacementMatrixComparator(IndexingFunction<X>, double[][]) - Constructor for class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
startColumn - Variable in class de.citec.tcs.alignment.visualization.SourceCodeColumn.CodePosition
 
startLine - Variable in class de.citec.tcs.alignment.visualization.SourceCodeColumn.CodePosition
 
STDKEYWORD - Static variable in class de.citec.tcs.alignment.wrappers.VectorialSequences
 
StrictADPCooptimalAlgorithm<X,Y,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This algorithm calculates all co-optimal paths in form of a CooptimalModel
StrictADPCooptimalAlgorithm(Grammar<N>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.adp.StrictADPCooptimalAlgorithm
 
StrictADPFullAlgorithm<X,Y,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This algorithm calculates an optimal AlignmentPath using the given ADP grammar and algebra/AlignmentSpecification.
StrictADPFullAlgorithm(Grammar<N>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.adp.StrictADPFullAlgorithm
 
StrictADPScoreAlgorithm<X,Y,N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
This algorithm calculates the strict alignment score for the given input grammar and algebra/AlignmentSpecification.
StrictADPScoreAlgorithm(Grammar<N>, Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.adp.StrictADPScoreAlgorithm
 
StrictAlignmentAllOptimalAlgorithm<X,Y> - Class in de.citec.tcs.alignment
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
StrictAlignmentAllOptimalAlgorithm(Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.StrictAlignmentAllOptimalAlgorithm
 
StrictAlignmentFullAlgorithm<X,Y> - Class in de.citec.tcs.alignment
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
StrictAlignmentFullAlgorithm(Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm
 
StrictAlignmentScoreAlgorithm<X,Y> - Class in de.citec.tcs.alignment
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
StrictAlignmentScoreAlgorithm(Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
 
StrictDTWFullAlgorithm<X,Y> - Class in de.citec.tcs.alignment
This is an implementation of the AbstractStrictDTWAlgorithm to calculate just one exemplary optimal DTW Alignment.
StrictDTWFullAlgorithm(Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.StrictDTWFullAlgorithm
 
StrictDTWScoreAlgorithm<X,Y> - Class in de.citec.tcs.alignment
This is an implementation of the AbstractStrictDTWAlgorithm to calculate just the normalized score.
StrictDTWScoreAlgorithm(Comparator<X, Y>) - Constructor for class de.citec.tcs.alignment.StrictDTWScoreAlgorithm
 
StringColumn<X,Y> - Class in de.citec.tcs.alignment.visualization
Applies 'toString' to visualize content in an HTML visualization.
StringColumn(String) - Constructor for class de.citec.tcs.alignment.visualization.StringColumn
 
StringComparatorWrapper - Class in de.citec.tcs.alignment.comparators
This is a wrapper for Comparators on StringValues.
StringComparatorWrapper(String, Comparator<String, String>) - Constructor for class de.citec.tcs.alignment.comparators.StringComparatorWrapper
 
StringEditDistance - Class in de.citec.tcs.alignment.wrappers
This is a simple wrapper to support an easier interface for the simple StringEditDistance problem.
StringEditDistance() - Constructor for class de.citec.tcs.alignment.wrappers.StringEditDistance
 
StringKeywordSpecification - Class in de.citec.tcs.alignment.sequence
This specifies String keywords which are not especially restricted.
StringKeywordSpecification(String) - Constructor for class de.citec.tcs.alignment.sequence.StringKeywordSpecification
 
Strings - Class in de.citec.tcs.alignment.primitives
This class provides static functions to transform strings into lists of characters.
StringValue - Class in de.citec.tcs.alignment.sequence
This value is supposed to represent strings that are not restricted to a certain alphabet.
StringValue() - Constructor for class de.citec.tcs.alignment.sequence.StringValue
 
StringValue(String) - Constructor for class de.citec.tcs.alignment.sequence.StringValue
 
StringVisualizer<X,Y> - Class in de.citec.tcs.alignment.visualization
This is a trivial Visualizer that just calls the toString() method of AlignmentPath.
StringVisualizer() - Constructor for class de.citec.tcs.alignment.visualization.StringVisualizer
 
supports(OperationType) - Method in class de.citec.tcs.alignment.comparators.AbstractValueComparatorWrapper
 
supports(OperationType) - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
supports(OperationType) - Method in interface de.citec.tcs.alignment.comparators.Comparator
This method should return true if and only if this Comparator supports the given alignment operation.
supports(OperationType) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
 
supports(OperationType) - Method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
 
SymbolicComparatorWrapper - Class in de.citec.tcs.alignment.comparators
This is a wrapper for Comparators on SymbolicValues.
SymbolicComparatorWrapper(String, Comparator<String, String>) - Constructor for class de.citec.tcs.alignment.comparators.SymbolicComparatorWrapper
 
SymbolicKeywordSpecification - Class in de.citec.tcs.alignment.sequence
This specifies symbolic keywords by their alphabet.
SymbolicKeywordSpecification(Alphabet, String) - Constructor for class de.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
 
SymbolicValue - Class in de.citec.tcs.alignment.sequence
This is a special value class that is restricted to a finite list of values defined by an alphabet.
SymbolicValue(Alphabet) - Constructor for class de.citec.tcs.alignment.sequence.SymbolicValue
 
SymbolicValue(Alphabet, String) - Constructor for class de.citec.tcs.alignment.sequence.SymbolicValue
 

T

toMatrix() - Method in class de.citec.tcs.alignment.Alignment
This transforms the Alignment to a matrix, mostly for visualization purposes.
toMatrix() - Method in class de.citec.tcs.alignment.AlignmentList
This transforms the AlignmentList to a matrix, mostly for visualization purposes.
toMatrix() - Method in class de.citec.tcs.alignment.AlignmentMap
This transforms the AlignmentMap to a matrix, mostly for visualization purposes.
toSequences(String[]) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
toSequences(Collection<String>) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
toSequences(String[], Alphabet) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
Transforms the given strings to the TCSAlignmentToolbox Sequence format using the given alphabet.
toSequences(Collection<String>, Alphabet) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
Transforms the given strings to the TCSAlignmentToolbox Sequence format using the given alphabet.
toSequences(double[][]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Transforms the given arrays to sequences.
toSequences(double[][][]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Transforms the given arrays to sequences.
toSequences(double[][][], String[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Transforms the given arrays to sequences.
toSequences(double[][][], String[], int[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
Transforms the given arrays to sequences.
toString() - Method in class de.citec.tcs.alignment.adp.DPCellId
 
toString(Enum[]) - Method in class de.citec.tcs.alignment.adp.DPCellId
 
toString() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar.RuleAvailabilityMatrix
 
toString() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
 
toString() - Method in class de.citec.tcs.alignment.adp.ProductionRule
 
toString() - Method in class de.citec.tcs.alignment.Alignment
 
toString() - Method in class de.citec.tcs.alignment.comparators.AlignmentSpecification
 
toString() - Method in class de.citec.tcs.alignment.Operation
 
toString() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine.MatrixCoordinate
 
toString() - Method in class de.citec.tcs.alignment.sequence.Alphabet
 
toString() - Method in class de.citec.tcs.alignment.sequence.KeywordSpecification
 
toString() - Method in class de.citec.tcs.alignment.sequence.NodeSpecification
 
toString() - Method in class de.citec.tcs.alignment.sequence.Sequence
 
toString() - Method in class de.citec.tcs.alignment.sequence.StringValue
 
toString() - Method in class de.citec.tcs.alignment.sequence.SymbolicValue
 
toString() - Method in class de.citec.tcs.alignment.sequence.VectorialValue
 
transform(double[]) - Static method in class de.citec.tcs.alignment.primitives.Doubles
Returns a list containing one-dimensional double arrays, one for each entry in the given array.
transform(double[][]) - Static method in class de.citec.tcs.alignment.primitives.Doubles
Returns a list containing a list of doubles for each row in the given double matrix.
transform(List<double[]>) - Static method in class de.citec.tcs.alignment.primitives.Doubles
Returns a list containing a list of doubles for each double array in the given list.
transform(double[][][]) - Static method in class de.citec.tcs.alignment.primitives.Doubles
Returns a list containing a list of double arrays for each entry in the given tensor of doubles.
transform(Object[]) - Static method in class de.citec.tcs.alignment.primitives.Doubles
Returns a list containing a list of double arrays for each entry in the given Object array.
transform(String) - Static method in class de.citec.tcs.alignment.primitives.Strings
Returns the characters of the given string as a list.
transform(char[]) - Static method in class de.citec.tcs.alignment.primitives.Strings
Returns the characters of the given array as a list.
transform(String[]) - Static method in class de.citec.tcs.alignment.primitives.Strings
Returns a list, containing a list of characters for each of the given strings.
transform(List<String>) - Static method in class de.citec.tcs.alignment.primitives.Strings
Returns a list, containing a list of characters for each of the given strings.
transform(char[][]) - Static method in class de.citec.tcs.alignment.primitives.Strings
Returns a list, containing a list of characters for each of the given character arrays.
transformToResult(double[][], double[][], double[], double[], List<X>, List<Y>) - Method in class de.citec.tcs.alignment.AbstractStrictAlignmentAlgorithm
This method has to be implemented by sub classes to transform a calculated dynamic programming matrix to a valid result of that implementation.
transformToResult(double[][], double[][], double[][], double[][], List<X>, List<Y>) - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
This method has to be implemented by sub classes to transform a calculated dynamic programming matrix to a valid result of that implementation.
transformToResult(EnumMap<N, double[][]>, EnumMap<OperationType, double[][]>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
This method should not be called from outside! The subclass uses this method to transform the alignment matrix and the input sequences to the actual alignment result.
transformToResult(EnumMap<N, double[][]>, EnumMap<OperationType, double[][]>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.SoftADPFullAlgorithm
 
transformToResult(EnumMap<N, double[][]>, EnumMap<OperationType, double[][]>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.SoftADPScoreAlgorithm
 
transformToResult(EnumMap<N, SparseAbstractADPAlgorithm.SparseMatrix>, EnumMap<OperationType, SparseAbstractADPAlgorithm.SparseMatrix>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm
This method should not be called from outside! The subclass uses this method to transform the alignment matrix and the input sequences to the actual alignment result.
transformToResult(EnumMap<N, SparseAbstractADPAlgorithm.SparseMatrix>, EnumMap<OperationType, SparseAbstractADPAlgorithm.SparseMatrix>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.SparseStrictADPFullAlgorithm
 
transformToResult(EnumMap<N, SparseAbstractADPAlgorithm.SparseMatrix>, EnumMap<OperationType, SparseAbstractADPAlgorithm.SparseMatrix>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.SparseStrictADPScoreAlgorithm
 
transformToResult(EnumMap<N, double[][]>, EnumMap<OperationType, double[][]>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.StrictADPCooptimalAlgorithm
 
transformToResult(EnumMap<N, double[][]>, EnumMap<OperationType, double[][]>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.StrictADPFullAlgorithm
 
transformToResult(EnumMap<N, double[][]>, EnumMap<OperationType, double[][]>, EnumMap<OperationType, double[]>, EnumMap<OperationType, double[]>, List<X>, List<Y>) - Method in class de.citec.tcs.alignment.adp.StrictADPScoreAlgorithm
 
transformToResult(double[][], double[][], double[], double[], List<X>, List<Y>) - Method in class de.citec.tcs.alignment.StrictAlignmentAllOptimalAlgorithm
 
transformToResult(double[][], double[][], double[], double[], List<X>, List<Y>) - Method in class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm
 
transformToResult(double[][], double[][], double[], double[], List<X>, List<Y>) - Method in class de.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
 
transformToResult(double[][], double[][], double[][], double[][], List<X>, List<Y>) - Method in class de.citec.tcs.alignment.StrictDTWFullAlgorithm
 
transformToResult(double[][], double[][], double[][], double[][], List<X>, List<Y>) - Method in class de.citec.tcs.alignment.StrictDTWScoreAlgorithm
 
TrivialEditComparator<X> - Class in de.citec.tcs.alignment.comparators
This is a Comparator for SymbolicValues that just specifies a score for: the deletion of a symbol (1 per default) the insertion of a symbol (1 per default) the skip deletion of a symbol (0.5 per default) the skip insertion of a symbol (0.5 per default) a match between the same symbols (0 per default) a mismatch between different symbols (1 per default) Please note that this is just a special case of the much more general ReplacementComparator.
TrivialEditComparator() - Constructor for class de.citec.tcs.alignment.comparators.TrivialEditComparator
 
TRUE - Static variable in class de.citec.tcs.alignment.learning.DistanceIndex
This trivial IndexFilter returns always true.

V

validate(Grammar, Comparator) - Static method in class de.citec.tcs.alignment.adp.ComparatorValidator
Checks whether the given Comparator supports all OperationType the given Grammar requires and throws an IllegalArgumentException if it does not.
validate() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
This ensures that the grammar is terminal, that is: 1.) There is at least one possible path of production rules that leads from the axiom to an accepting nonterminal.
validate(AlignmentAlgorithm<X, Y, ?>, Comparator<? extends X, ? extends Y>) - Static method in class de.citec.tcs.alignment.ComparatorValidator
Checks whether the given Comparator supports all OperationType the given AlignmentAlgorithm requires and throws an IllegalArgumentException if it does not.
validate(Value) - Method in class de.citec.tcs.alignment.sequence.KeywordSpecification
Returns true if the given value is in order according to this specification, meaning that it has the correct type or is null.
validate(Value) - Method in class de.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
This applies the KeywordSpecification validation and additionally checks whether the given value is part of the Alphabet.
validate(Value) - Method in class de.citec.tcs.alignment.sequence.VectorialKeywordSpecification
This applies the KeywordSpecification validation and additionally checks whether the given value has the correct length.
Value - Interface in de.citec.tcs.alignment.sequence
This represents a single value for a keyword in a given node.
ValueColumn - Class in de.citec.tcs.alignment.visualization
This creates a HTML column containing the string representation of values in the left/right node of the input operation for the given keyword.
ValueColumn(String) - Constructor for class de.citec.tcs.alignment.visualization.ValueColumn
 
ValueComparator - Interface in de.citec.tcs.alignment.comparators
An interface for comparators on Values as defined in the sequence module.
valueOf(String) - Static method in enum de.citec.tcs.alignment.adp.AffineGrammar.Nonterminal
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.citec.tcs.alignment.adp.DTWGrammar.Nonterminal
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar.Nonterminal
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.citec.tcs.alignment.adp.GlobalGrammar.Nonterminal
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar.Nonterminal
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.citec.tcs.alignment.comparators.NCDComparator.CompressorType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.citec.tcs.alignment.comparators.OperationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.citec.tcs.alignment.DissimilarityWeighting
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.citec.tcs.alignment.sequence.ValueType
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.citec.tcs.alignment.adp.AffineGrammar.Nonterminal
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.citec.tcs.alignment.adp.DTWGrammar.Nonterminal
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar.Nonterminal
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.citec.tcs.alignment.adp.GlobalGrammar.Nonterminal
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.citec.tcs.alignment.adp.SakoeChibaDTWGrammar.Nonterminal
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.citec.tcs.alignment.comparators.NCDComparator.CompressorType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.citec.tcs.alignment.comparators.OperationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.citec.tcs.alignment.DissimilarityWeighting
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.citec.tcs.alignment.sequence.ValueType
Returns an array containing the constants of this enum type, in the order they are declared.
ValueType - Enum in de.citec.tcs.alignment.sequence
This defines all possible types of values.
VectorialComparatorWrapper - Class in de.citec.tcs.alignment.comparators
This is a wrapper for Comparators on VectorialValues.
VectorialComparatorWrapper(String, Comparator<double[], double[]>) - Constructor for class de.citec.tcs.alignment.comparators.VectorialComparatorWrapper
 
VectorialKeywordSpecification - Class in de.citec.tcs.alignment.sequence
This specifies vectors by their length.
VectorialKeywordSpecification(int, String) - Constructor for class de.citec.tcs.alignment.sequence.VectorialKeywordSpecification
 
VectorialSequences - Class in de.citec.tcs.alignment.wrappers
This provides an easier interface for simple vectorial sequences.
VectorialSequences() - Constructor for class de.citec.tcs.alignment.wrappers.VectorialSequences
 
VectorialValue - Class in de.citec.tcs.alignment.sequence
This value is reserved for numeric vectors, represented internally as doubles.
VectorialValue() - Constructor for class de.citec.tcs.alignment.sequence.VectorialValue
 
VectorialValue(double[]) - Constructor for class de.citec.tcs.alignment.sequence.VectorialValue
 
VectorialValue(Object) - Constructor for class de.citec.tcs.alignment.sequence.VectorialValue
 
vectorToCostMatrix(double[]) - Static method in class de.citec.tcs.alignment.comparators.SquareReplacementMatrixComparator
Turns a parameter vector into a cost matrix Lambda.
visualize(Alignment<Character, Character>, OutputStream) - Method in class de.citec.tcs.alignment.visualization.CharacterVisualizer
 
visualize(X) - Method in interface de.citec.tcs.alignment.visualization.ElementHTMLVisualizer
Transforms an object into a HTML string.
visualize(Alignment<X, Y>, OutputStream) - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
 
visualize(Alignment<X, Y>, OutputStream) - Method in class de.citec.tcs.alignment.visualization.StringVisualizer
 
visualize(Alignment<X, Y>, OutputStream) - Method in interface de.citec.tcs.alignment.visualization.Visualizer
Visualize the given Alignment and write the resulting data to the given OutputStream.
visualize(Visualizer<X, Y>, Alignment<X, Y>, Writer) - Static method in class de.citec.tcs.alignment.visualization.VisualizerUtils
Visualize the given Alignment and write the resulting data to the given Writer.
visualize(Visualizer<X, Y>, Alignment<X, Y>, File) - Static method in class de.citec.tcs.alignment.visualization.VisualizerUtils
Visualize the given Alignment and write the resulting data to the given File.
visualize(Visualizer<X, Y>, Alignment<X, Y>, String) - Static method in class de.citec.tcs.alignment.visualization.VisualizerUtils
Visualize the given Alignment and write the resulting data to the given File.
visualize(Visualizer<X, Y>, Alignment<X, Y>) - Static method in class de.citec.tcs.alignment.visualization.VisualizerUtils
Visualize the given Alignment and write the resulting data to a String.
visualizeMatrix(Alignment[][], String[], File) - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
This takes a full or sparse matrix of Alignments and provides HTML output for it.
visualizeMatrix(Alignment[][], String[], String[], File) - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
This takes a full or sparse matrix of Alignments and provides HTML output for it.
Visualizer<X,Y> - Interface in de.citec.tcs.alignment.visualization
This is an interface for visualizers.
VisualizerUtils - Class in de.citec.tcs.alignment.visualization
Some Utility Functions for Visualizers.

W

writeFromClassPath(String, Writer) - Static method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
Writes the data found at the given path in the class path to the given writer.
writeFromClassPath(Class, String, Writer) - Static method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
Writes the data found at the given path in the class path to the given writer.

Z

ZeroNormComparator - Class in de.citec.tcs.alignment.comparators
This comparator works on basis of the zero norm.
ZeroNormComparator(int) - Constructor for class de.citec.tcs.alignment.comparators.ZeroNormComparator
 
ZeroNormComparator(int, double) - Constructor for class de.citec.tcs.alignment.comparators.ZeroNormComparator
 
ZeroNormComparator(double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.ZeroNormComparator
 
ZeroNormComparator(double[], double[], double[], double[]) - Constructor for class de.citec.tcs.alignment.comparators.ZeroNormComparator
 
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Copyright (C) 2016 Benjamin Paaßen, AG Theoretical Computer Science, Centre of Excellence Cognitive Interaction Technology (CITEC), University of Bielefeld, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/tcs . This documentation is licensed under the conditions of CC-BY-SA 4.0: https://creativecommons.org/licenses/by-sa/4.0/