- 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 and 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.
- AndFilter(DistanceIndex.IndexFilter, DistanceIndex.IndexFilter) - Constructor for class de.citec.tcs.alignment.learning.DistanceIndex.AndFilter
-
- 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.
- 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.
- CalculationResult(I, R) - Constructor for class de.citec.tcs.alignment.parallel.Engine.CalculationResult
-
- 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.
- CodePosition(String, int, int, int, int) - Constructor for class de.citec.tcs.alignment.visualization.SourceCodeColumn.CodePosition
-
- 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
-
- 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.IdentityFilter - Class in de.citec.tcs.alignment.learning
-
This filter returns true if the input index is equal to the reference
index.
- 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.NotFilter - Class in de.citec.tcs.alignment.learning
-
Returns true if and only if the underlying filter returns false.
- 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
-
- 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
-
- 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
-
- IdentityFilter(int) - Constructor for class de.citec.tcs.alignment.learning.DistanceIndex.IdentityFilter
-
- 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.
- Integers - Class in de.citec.tcs.alignment.primitives
-
This class provides static functions to transform integer arrays to lists of Integers.
- 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.
- 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
-
- NotFilter(DistanceIndex.IndexFilter) - Constructor for class de.citec.tcs.alignment.learning.DistanceIndex.NotFilter
-
- 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/Comparator.
- 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/Comparator.
- 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.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.
- 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.
- SparseMatrix() - Constructor for class de.citec.tcs.alignment.adp.SparseAbstractADPAlgorithm.SparseMatrix
-
- 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/Comparator.
- 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/Comparator.
- 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/Comparator.
- 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/Comparator.
- 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
-
- 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(boolean[][]) - Static method in class de.citec.tcs.alignment.primitives.Booleans
-
Returns a list of lists of Booleans, one list per row in the given matrix.
- transform(List<boolean[]>) - Static method in class de.citec.tcs.alignment.primitives.Booleans
-
Returns a list of lists of Booleans, one list per boolean array in the given list.
- 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(int[][]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns a list of lists of Integers, one list per row in the given matrix.
- transform(List<int[]>) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns a list of lists of Integers, one list per integer array in the given 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.
- transform(Character[][]) - 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.
- transformObjects(Object[]) - Static method in class de.citec.tcs.alignment.primitives.Booleans
-
Returns a list of lists of integers, one for each object in the given array.
- transformObjects(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.
- transformObjects(Object[]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns a list of lists of integers, one for each object in the given array.
- transformObjects(Object[]) - Static method in class de.citec.tcs.alignment.primitives.Strings
-
Returns a list containing a list of characters for each entry in the given Object array.
- transformSingle(boolean[]) - Static method in class de.citec.tcs.alignment.primitives.Booleans
-
Returns the Booleans contained in the given array as a list.
- transformSingle(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.
- transformSingle(double[][]) - Static method in class de.citec.tcs.alignment.primitives.Doubles
-
Transforms the given matrix of doubles into a list of doubles.
- transformSingle(int[]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns the integers contained in the given array as a list.
- transformSingle(short[]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns the integers contained in the given array as a list.
- transformSingle(char[]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns the integers contained in the given array as a list.
- transformSingle(byte[]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns the integers contained in the given array as a list.
- transformSingle(Integer[]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns the integers contained in the given array as a list.
- transformSingle(Short[]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns the integers contained in the given array as a list.
- transformSingle(Character[]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns the integers contained in the given array as a list.
- transformSingle(Byte[]) - Static method in class de.citec.tcs.alignment.primitives.Integers
-
Returns the integers contained in the given array as a list.
- transformSingle(String) - Static method in class de.citec.tcs.alignment.primitives.Strings
-
Returns the characters of the given string as a list.
- transformSingle(char[]) - Static method in class de.citec.tcs.alignment.primitives.Strings
-
Returns the characters of the given array as a list.
- 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.
- 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.