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

A

AbstractGapAlignmentAlgorithm<X extends AlignmentMatrixEntry,R> - Class in de.unibi.citec.tcs.alignment
This is an abstract super class for GapAlignmentAlgorithms that provides a generic implementation of the dynamic programming needed to efficiently calculate the alignment.
AbstractGapAlignmentAlgorithm(AlignmentSpecification, Class<X>, Class<R>) - Constructor for class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
 
AbstractHTMLTransformerFromPath - Class in de.unibi.citec.tcs.alignment.visualization
 
AbstractHTMLTransformerFromPath(String) - Constructor for class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
Attention: when using this constructor, you have to call setFiles() manually.
AbstractHTMLTransformerFromPath(String, String[]) - Constructor for class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
Initializes given files or folders.
AbstractHTMLTransformerFromPath(String, String) - Constructor for class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
Initializes given folder.
AbstractHTMLTransformerFromPath(String, File[]) - Constructor for class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
Initializes given files or folders.
AbstractHTMLTransformerFromPath(String, File) - Constructor for class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
Initializes given folder.
AbstractLocalAlignmentAlgorithm<R> - Class in de.unibi.citec.tcs.alignment
This is an implementation of the local alignment algorithm scheme combining actually two approaches: First the algorithm of Gotoh et al.
AbstractLocalAlignmentAlgorithm(Class<R>, AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
 
AbstractLocalAlignmentAlgorithm.Recurrence - Enum in de.unibi.citec.tcs.alignment
 
AbstractSpecialHTMLTransformer - Class in de.unibi.citec.tcs.alignment.visualization
 
AbstractSpecialHTMLTransformer(String) - Constructor for class de.unibi.citec.tcs.alignment.visualization.AbstractSpecialHTMLTransformer
Takes the keyword that serves as column header for the visualization.
AbstractStrictDTWAlgorithm<R> - Class in de.unibi.citec.tcs.alignment
This serves as an abstract super class for strict Dynamic Time Warping implementations.
AbstractStrictDTWAlgorithm(Class<R>, AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.AbstractStrictDTWAlgorithm
 
AbstractValue - Class in de.unibi.citec.tcs.alignment.sequence
This is a convenience implementation of the Value interface.
AbstractValue(ValueType) - Constructor for class de.unibi.citec.tcs.alignment.sequence.AbstractValue
 
add(int, double) - Method in interface de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative
This adds a new derivative to this sparse representation.
add(int, double) - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.EmptySparseLocalEntry
This adds a new derivative to this sparse representation.
add(int, double) - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FixedSparseLocalDerivative
This adds a new derivative to this sparse representation.
add(int, double) - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FlexibleSparseLocalDerivative
This adds a new derivative to this sparse representation.
add(int, double) - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.TrivialSparseLocalDerivative
This adds a new derivative to this sparse representation.
add(SpecialHTMLTransformer, Sequence) - Method in class de.unibi.citec.tcs.alignment.visualization.ExternalContent
Adds content for the key to this ExternalContent.
AlignmentAlgorithm<R> - Interface in de.unibi.citec.tcs.alignment
This is the most generic AlignmentAlgorithm interface for all algorithms that provide some sort of alignment between two input sequences.
AlignmentDerivativeAlgorithm - Interface in de.unibi.citec.tcs.alignment
This is an interface to provide calculation methods for the derivative of an alignment w.r.t. a specific comparator and the weights for the keywords.
AlignmentMatrixEntry - Interface in de.unibi.citec.tcs.alignment
This is an interface for the entries of an alignment matrix.
AlignmentPath - Class in de.unibi.citec.tcs.alignment
This class models an alignment path as it is given out by a strict alignment.
AlignmentPath(AlignmentSpecification, Sequence, Sequence, double) - Constructor for class de.unibi.citec.tcs.alignment.AlignmentPath
 
AlignmentSpecification - Class in de.unibi.citec.tcs.alignment
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(NodeSpecification) - Constructor for class de.unibi.citec.tcs.alignment.AlignmentSpecification
Initializes an alignment specification from a given node specification.
AlignmentSpecification(Sequence) - Constructor for class de.unibi.citec.tcs.alignment.AlignmentSpecification
Initializes an alignment specification using the node specification inside.
AlignmentSpecification(NodeSpecification, String[], Comparator[]) - Constructor for class de.unibi.citec.tcs.alignment.AlignmentSpecification
 
AlignmentSpecification(NodeSpecification, String[], Comparator[], double[]) - Constructor for class de.unibi.citec.tcs.alignment.AlignmentSpecification
 
Alphabet - Class in de.unibi.citec.tcs.alignment.sequence
An alphabet is an ordered set of arbitrary symbols.
Alphabet(HashMap<String, Integer>) - Constructor for class de.unibi.citec.tcs.alignment.sequence.Alphabet
 
Alphabet(String) - Constructor for class de.unibi.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.unibi.citec.tcs.alignment.sequence.Alphabet
Constructs an IndexingScheme from a mapping of indices to strings.
averageScore() - Method in class de.unibi.citec.tcs.alignment.PathMap
Returns the average score according to the given weighting scheme.

C

calc_weighted_comp_sum(Comparator[], double[], int[], Node, Node) - Static method in class de.unibi.citec.tcs.alignment.SoftDTWModel
Returns weighted sum k of local comparators: k = sum(w_i * k_i) with: k_i: local comparators w_i: local weights Note: Comparators, weights, originalIndices are supposed to originate from the same AlignmentSpecification.
calculate() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
This starts the calculation of the pairwise alignment of the input Sequencs according to the given algorithm.
calculateAlignment(Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This calculates the alignment between the Sequences a and b and returns it as an instance of the result class for this algorithm.
calculateAlignment(Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
This calculates the alignment between the Sequences a and b and returns it as an instance of the result class for this algorithm.
calculateAlignment(Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.AbstractStrictDTWAlgorithm
This calculates the alignment between the Sequences a and b and returns it as an instance of the result class for this algorithm.
calculateAlignment(Sequence, Sequence) - Method in interface de.unibi.citec.tcs.alignment.AlignmentAlgorithm
This calculates the alignment between the Sequences a and b and returns it as an instance of the result class for this algorithm.
calculateAlignment(Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.DynamicTimeWarpingAlgorithm
This calculates the alignment between the Sequences a and b and returns it as an instance of the result class for this algorithm.
calculateComparatorDerivatives(DerivableComparator<?, R>, String) - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
 
calculateCompressedSize(String) - Method in enum de.unibi.citec.tcs.alignment.comparators.NCDComparator.CompressorType
Calculates the compressed size of the given input string in bytes.
calculateDeletionCosts(Node, AlignmentSpecification) - Static method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This calculates the non-weighted costs for deleting the single values in node a.
calculateDerivative(AlignmentAlgorithm<? extends AlignmentDerivativeAlgorithm>, Sequence, Sequence) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
Calculates the alignment derivative between the two given input sequences using the given algorithm.
calculateDerivatives(AlignmentAlgorithm<R>, Sequence[], int) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
Calculates the pairwise alignment derivative between all given input sequences using the given algorithm.
calculateInsertionCosts(Node, AlignmentSpecification) - Static method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This calculates the non-weighted costs for inserting the single values of node b.
calculateLocalDerivative(int, V, V, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
This is called by an AlignmentDerivativeAlgorithm and should calculate the local derivative for only one comparison of the values a and b.
calculateLocalDerivative(int, X, X, OperationType) - Method in interface de.unibi.citec.tcs.alignment.comparators.DerivableComparator
This is called by an AlignmentDerivativeAlgorithm and should calculate the local derivative for only one comparison of the values a and b.
calculateLocalDerivative(int, VectorialValue, VectorialValue, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
TODO: think about opterationType This is called by an AlignmentDerivativeAlgorithm and should calculate the local derivative for only one comparison of the values a and b.
calculateLocalDerivative(int, SymbolicValue, SymbolicValue, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
This is called by an AlignmentDerivativeAlgorithm and should calculate the local derivative for only one comparison of the values a and b.
calculateLocalDerivative(int, V, V, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This is called by an AlignmentDerivativeAlgorithm and should calculate the local derivative for only one comparison of the values a and b.
calculateNCD(String, String) - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
Returns the normalized compression distance between two input strings according to the compressor currently set.
calculateParameterDerivative(DerivableComparator<X, Y>, String) - Method in interface de.unibi.citec.tcs.alignment.AlignmentDerivativeAlgorithm
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.PathList
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.PathMap
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateRawParameterDerivative(DerivableComparator<X, Y>, String) - Method in interface de.unibi.citec.tcs.alignment.AlignmentDerivativeAlgorithm
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateRawParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateRawParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.PathList
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateRawParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.PathMap
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateRawParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateRawParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateRawParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
This returns the derivatives for all parameters of the given comparator according to the implementation.
calculateReplacementCosts(Node, Node, AlignmentSpecification) - Static method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This calculates the non-weighted costs for replacing the single values in node a by the values in node b.
calculateSkipDeletionCosts(Node, AlignmentSpecification) - Static method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
This calculates the non-weighted costs for skip-deleting the single values in node a.
calculateSkipInsertionCosts(Node, AlignmentSpecification) - Static method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
This calculates the non-weighted costs for skip-inserting the single values of node b.
calculateSoftminDerivatives(double, double[]) - Static method in class de.unibi.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.unibi.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.unibi.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.unibi.citec.tcs.alignment.Softmin
Calculates the softmin probabilities p_i for the given beta and the given variables.
calculateSparseLocalDerivative(V, V, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
This method shall return a sparse representation of the derivative for all parameters that have non-zero derivatives in this step of the alignment.
calculateSparseLocalDerivative(SymbolicValue, SymbolicValue, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
This method shall return a sparse representation of the derivative for all parameters that have non-zero derivatives in this step of the alignment.
calculateSparseLocalDerivative(V, V, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This method shall return a sparse representation of the derivative for all parameters that have non-zero derivatives in this step of the alignment.
calculateSparseLocalDerivative(X, X, OperationType) - Method in interface de.unibi.citec.tcs.alignment.comparators.SparseDerivableComparator
This method shall return a sparse representation of the derivative for all parameters that have non-zero derivatives in this step of the alignment.
calculateWeightDerivative() - Method in interface de.unibi.citec.tcs.alignment.AlignmentDerivativeAlgorithm
Calculates the derivative for each keyword weight.
calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
Calculates the derivative for each keyword weight.
calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.PathList
Calculates the derivative for each keyword weight.
calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.PathMap
Calculates the derivative for each keyword weight.
calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
Calculates the derivative for each keyword weight.
calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
Calculates the derivative for each keyword weight.
calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
Calculates the derivative for each keyword weight.
calculateWeightDerivatives() - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
This calculates the weight derivatives for each of the input AlignmentDerivativeAlgorithms.
calculateWeighting(Collection<Double>) - Method in enum de.unibi.citec.tcs.alignment.ScoreBasedWeighting
 
calculateWeighting(double[]) - Method in enum de.unibi.citec.tcs.alignment.ScoreBasedWeighting
This calculates the normalized weights (between 0 and 1 and adding up to 1) for the given scores.
CharStatComparator - Class in de.unibi.citec.tcs.alignment.comparators
This compares strings using statistics over the number of letters inside.
CharStatComparator() - Constructor for class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
 
choice(double...) - Method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
This should implement the choice function as the term is used in the Bellman's Gap context.
choice(double...) - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentFullAlgorithm
This implements the strict maximum of the given input doubles.
choice(double...) - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentScoreAlgorithm
This implements the strict maximum of the given input doubles.
choice(double...) - Method in class de.unibi.citec.tcs.alignment.StrictLocalAlignmentFullAlgorithm
This implements the strict maximum of the given input doubles.
choice(double...) - Method in class de.unibi.citec.tcs.alignment.StrictLocalAlignmentScoreAlgorithm
This implements the strict maximum of the given input doubles.
CLASSNAME_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 
clone() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
CODEPOSITION_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 
Comparator<X extends Value> - Interface in de.unibi.citec.tcs.alignment.comparators
This defines a function that returns a normalized distance between two objects.
compare(StringValue, StringValue) - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
This has to return a distance between a and b with the following restrictions: The return value has to lie between 0 and 1.
compare(X, X) - Method in interface de.unibi.citec.tcs.alignment.comparators.Comparator
This has to return a distance between a and b with the following restrictions: The return value has to lie between 0 and 1.
compare(VectorialValue, VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
This has to return a distance between a and b with the following restrictions: The return value has to lie between 0 and 1.
compare(VectorialValue, VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
This has to return a distance between a and b with the following restrictions: The return value has to lie between 0 and 1.
compare(VectorialValue, VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
This has to return a distance between a and b with the following restrictions: The return value has to lie between 0 and 1.
compare(StringValue, StringValue) - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
This has to return a distance between a and b with the following restrictions: The return value has to lie between 0 and 1.
compare(SymbolicValue, SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
This has to return a distance between a and b with the following restrictions: The return value has to lie between 0 and 1.
compare(SymbolicValue, SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
This has to return a distance between a and b with the following restrictions: The return value has to lie between 0 and 1.
ComparisonBasedSkipExtendedComparator<V extends Value> - Class in de.unibi.citec.tcs.alignment.comparators
This is an abstract class allowing to define a dynamic method to extend a simple Comparator to a SkipComparator.
ComparisonBasedSkipExtendedComparator(V, V, V, V) - Constructor for class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
comparisonDerivative(int, StringValue, StringValue) - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
This should implement the local derivative calculation in case of comparisons.
comparisonDerivative(int, VectorialValue, VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
This should implement the local derivative calculation in case of comparisons.
comparisonDerivative(int, VectorialValue, VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
This should implement the local derivative calculation in case of comparisons.
comparisonDerivative(int, StringValue, StringValue) - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
This should implement the local derivative calculation in case of comparisons.
comparisonDerivative(int, V, V) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This should implement the local derivative calculation in case of comparisons.
comparisonDerivative(int, SymbolicValue, SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
This should implement the local derivative calculation in case of comparisons.
contains(String) - Method in class de.unibi.citec.tcs.alignment.visualization.ExternalContent
 
Counter - Class in de.unibi.citec.tcs.alignment
Just a very simple counting class.
Counter() - Constructor for class de.unibi.citec.tcs.alignment.Counter
 
Counter(int) - Constructor for class de.unibi.citec.tcs.alignment.Counter
 
createDelInitial(X, int, double) - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This method should not be called from outside!
createDelInitial(SoftPathModel.SoftMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
This method should not be called from outside!
createDelInitial(SoftPathModel.SoftMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
This method should not be called from outside!
createDelInitial(SoftAlignmentScoreAlgorithm.ScoreEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
This method should not be called from outside!
createDelInitial(StrictAlignmentFullAlgorithm.FullMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm
This method should not be called from outside!
createDelInitial(StrictAlignmentScoreAlgorithm.ScoreEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
This method should not be called from outside!
createDelInitial(StrictAllOptimalAlgorithm.FullMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
This method should not be called from outside!
createDelInitial(StrictAllOptimalAlgorithm.FullMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
This method should not be called from outside!
createGenericArray(int, Class<X>) - Static method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This circumvents Javas rule against generic array cration by using reflection.
createGenericMatrix(int, int, Class<X>) - Static method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This circumvents Javas rule against generic array cration by using reflection.
createHTMLs(AlignmentPath[][], ArrayList<String>, String, String, String[], ExternalContent[], boolean) - Static method in class de.unibi.citec.tcs.alignment.visualization.Visualization
Visualizes given alignments in clear and adaptable tables.
createInitial() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This method should not be called from outside!
createInitial() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
This method should not be called from outside!
createInitial() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
This method should not be called from outside!
createInitial() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
This method should not be called from outside!
createInitial() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm
This method should not be called from outside!
createInitial() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
This method should not be called from outside!
createInitial() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
This method should not be called from outside!
createInitial() - Method in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
This method should not be called from outside!
createInsInitial(X, int, double) - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This method should not be called from outside!
createInsInitial(SoftPathModel.SoftMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
This method should not be called from outside!
createInsInitial(SoftPathModel.SoftMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
This method should not be called from outside!
createInsInitial(SoftAlignmentScoreAlgorithm.ScoreEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
This method should not be called from outside!
createInsInitial(StrictAlignmentFullAlgorithm.FullMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm
This method should not be called from outside!
createInsInitial(StrictAlignmentScoreAlgorithm.ScoreEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
This method should not be called from outside!
createInsInitial(StrictAllOptimalAlgorithm.FullMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
This method should not be called from outside!
createInsInitial(StrictAllOptimalAlgorithm.FullMatrixEntry, int, double) - Method in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
This method should not be called from outside!
createNewEntry(X, X, X, int, int, double, double, double) - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This method should not be called from outside!
createNewEntry(SoftPathModel.SoftMatrixEntry, SoftPathModel.SoftMatrixEntry, SoftPathModel.SoftMatrixEntry, int, int, double, double, double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
This method should not be called from outside!
createNewEntry(SoftPathModel.SoftMatrixEntry, SoftPathModel.SoftMatrixEntry, SoftPathModel.SoftMatrixEntry, int, int, double, double, double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
This method should not be called from outside!
createNewEntry(SoftAlignmentScoreAlgorithm.ScoreEntry, SoftAlignmentScoreAlgorithm.ScoreEntry, SoftAlignmentScoreAlgorithm.ScoreEntry, int, int, double, double, double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
This method should not be called from outside!
createNewEntry(StrictAlignmentFullAlgorithm.FullMatrixEntry, StrictAlignmentFullAlgorithm.FullMatrixEntry, StrictAlignmentFullAlgorithm.FullMatrixEntry, int, int, double, double, double) - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm
This method should not be called from outside!
createNewEntry(StrictAlignmentScoreAlgorithm.ScoreEntry, StrictAlignmentScoreAlgorithm.ScoreEntry, StrictAlignmentScoreAlgorithm.ScoreEntry, int, int, double, double, double) - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
This method should not be called from outside!
createNewEntry(StrictAllOptimalAlgorithm.FullMatrixEntry, StrictAllOptimalAlgorithm.FullMatrixEntry, StrictAllOptimalAlgorithm.FullMatrixEntry, int, int, double, double, double) - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
This method should not be called from outside!
createNewEntry(StrictAllOptimalAlgorithm.FullMatrixEntry, StrictAllOptimalAlgorithm.FullMatrixEntry, StrictAllOptimalAlgorithm.FullMatrixEntry, int, int, double, double, double) - Method in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
This method should not be called from outside!

D

de.unibi.citec.tcs.alignment - package de.unibi.citec.tcs.alignment
This package contains the actual AlignmentAlgorithms as well as their return classes.
de.unibi.citec.tcs.alignment.comparators - package de.unibi.citec.tcs.alignment.comparators
This package contains comparators that define distances between Values.
de.unibi.citec.tcs.alignment.sequence - package de.unibi.citec.tcs.alignment.sequence
This package contains the definition of input Sequences for AlignmentAlgorithms.
de.unibi.citec.tcs.alignment.visualization - package de.unibi.citec.tcs.alignment.visualization
 
de.unibi.citec.tcs.alignment.wrappers - package de.unibi.citec.tcs.alignment.wrappers
 
DEFAULTALPHABET - Static variable in class de.unibi.citec.tcs.alignment.wrappers.RandomSequenceGenerator
 
DEFAULTAPPROXTHRESHOLD - Static variable in class de.unibi.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.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
 
DEFAULTBETA - Static variable in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
 
DEFAULTBETA - Static variable in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
 
DEFAULTBETA - Static variable in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentFullAlgorithm
 
DEFAULTBETA - Static variable in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentScoreAlgorithm
 
DEFAULTKEYWORD - Static variable in class de.unibi.citec.tcs.alignment.sequence.Sequence
 
DEFAULTPATHLIMIT - Static variable in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
 
DEFAULTPATHLIMIT - Static variable in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
 
DEFAULTPATHLIMIT - Static variable in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
 
DEFAULTSTRINGLENGTH - Static variable in class de.unibi.citec.tcs.alignment.wrappers.RandomSequenceGenerator
 
DEFAULTTHREADNUM - Static variable in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
 
DEFAULTTHREADNUM - Static variable in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
 
DEFAULTVECTORIALLENGTH - Static variable in class de.unibi.citec.tcs.alignment.wrappers.RandomSequenceGenerator
 
delete(V) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
This should be called during an alignment to retrieve the costs for a deletion of value a from the first sequence.
delete(X) - Method in interface de.unibi.citec.tcs.alignment.comparators.GapComparator
This should be called during an alignment to retrieve the costs for a deletion of value a from the first sequence.
delete(SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
This should be called during an alignment to retrieve the costs for a deletion of value a from the first sequence.
delete(V) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This should be called during an alignment to retrieve the costs for a deletion of value a from the first sequence.
DerivableComparator<X extends Value,Y> - Interface in de.unibi.citec.tcs.alignment.comparators
This is an interface for comparators that have derivable parameters.
distance(String, String) - Static method in class de.unibi.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[]) - Method in class de.unibi.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[]) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
Returns the L1-distance between the vectors a and b, given that they have the same length.
DTWKernelComparator - Class in de.unibi.citec.tcs.alignment.comparators
implements halved gauss-kernel k: k = exp(-1/2sigma^2 * |x-y|^2) /2, with |.| beeing the weighted euclidian distance k is positive definite
DTWKernelComparator(double[]) - Constructor for class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
 
DTWKernelComparator(double[], double) - Constructor for class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
 
DynamicTimeWarpingAlgorithm - Class in de.unibi.citec.tcs.alignment
Implements soft alignment DTW.
DynamicTimeWarpingAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.DynamicTimeWarpingAlgorithm
 

E

equals(Object) - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
equals(Object) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
equals(Object) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
equals(Object) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
equals(Object) - Method in class de.unibi.citec.tcs.alignment.comparators.ExponentialNormalizer
equals(Object) - Method in class de.unibi.citec.tcs.alignment.comparators.HyperbolicNormalizer
equals(Object) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
equals(Object) - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
equals(Object) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
equals(Object) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
equals(Object) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
equals(Object) - Method in class de.unibi.citec.tcs.alignment.MatrixCoordinate
equals(Object) - Method in class de.unibi.citec.tcs.alignment.Operation
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.AbstractValue
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.Node
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.NodeSpecification
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.Sequence
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.StringValue
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialKeywordSpecification
equals(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
equals(Object) - Method in class de.unibi.citec.tcs.alignment.SparseMatrix
EuclideanComparator - Class in de.unibi.citec.tcs.alignment.comparators
Compares vectors using the L2-Norm.
EuclideanComparator(int) - Constructor for class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(Normalizer, int) - Constructor for class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(int, double) - Constructor for class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(Normalizer, int, double) - Constructor for class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(VectorialValue, VectorialValue, VectorialValue, VectorialValue) - Constructor for class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
 
EuclideanComparator(Normalizer, VectorialValue, VectorialValue, VectorialValue, VectorialValue) - Constructor for class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
 
ExponentialNormalizer - Class in de.unibi.citec.tcs.alignment.comparators
This normalizes by using the function 1-exp(-beta*d)
ExponentialNormalizer(double) - Constructor for class de.unibi.citec.tcs.alignment.comparators.ExponentialNormalizer
 
ExponentialNormalizer() - Constructor for class de.unibi.citec.tcs.alignment.comparators.ExponentialNormalizer
 
EXTENDS_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 
EXTERNAL_DEPENDENCIES_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 
ExternalContent - Class in de.unibi.citec.tcs.alignment.visualization
ExternalContent holds a bunch of selfdefined keywords and their corresponding content for one sequence, thereby for example one solution graph.
ExternalContent() - Constructor for class de.unibi.citec.tcs.alignment.visualization.ExternalContent
 

F

formatNumber(int, int) - Static method in class de.unibi.citec.tcs.alignment.visualization.Utils
Formats a given Number by adding zeros at the beginning.

G

GapAlignmentAlgorithm<R> - Interface in de.unibi.citec.tcs.alignment
This is an interface for Alignment algorithms that use gaps (insertion and deletion operations) in the alignment.
GapComparator<X extends Value> - Interface in de.unibi.citec.tcs.alignment.comparators
This specifies the comparator interface slightly to include the case that entities might be deleted/inserted.
GAPDEFAULT - Static variable in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
generateSequences(int, int, int) - Static method in class de.unibi.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.unibi.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.unibi.citec.tcs.alignment.wrappers.RandomSequenceGenerator
This generates an AlignmentSpecification and implicitly a NodeSpecification for K keywords.
get(int, int) - Method in class de.unibi.citec.tcs.alignment.SparseMatrix
Returns the value stored at the given position or null if no value was stored there until now.
getAlgorithm() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
 
getAlgorithms() - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
 
getAllPaths() - Method in class de.unibi.citec.tcs.alignment.PathMap
Returns all paths stored in this map in order of their score (from good/low to bad/high).
getAlpha() - Method in class de.unibi.citec.tcs.alignment.comparators.HyperbolicNormalizer
 
getAlphabet() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
getAlphabet() - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
Returns the Alphabet that defines which symbols are allowed for this keyword.
getAlphabet() - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
Returns the Alphabet that defines which symbols are allowed for this keyword.
getApproxThreshold() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
Returns the threshold for which exponents within the softmin function will be disregarded.
getApproxThreshold() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
Returns the threshold for which exponents within the softmin function will be disregarded.
getApproxThreshold() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
For more information on the ApproxThreshold have a look at the Softmin class.
getApproxThreshold() - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentFullAlgorithm
For more information on the ApproxThreshold have a look at the Softmin class.
getApproxThreshold() - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentScoreAlgorithm
For more information on the ApproxThreshold have a look at the Softmin class.
getAverageScore() - Method in class de.unibi.citec.tcs.alignment.PathList
Returns the average score for all paths in this list.
getBeta() - Method in class de.unibi.citec.tcs.alignment.comparators.ExponentialNormalizer
 
getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
 
getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
 
getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
 
getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentFullAlgorithm
 
getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentScoreAlgorithm
 
getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
The parameter defining the "softness" of the alignment.
getCodeFileContent() - Method in class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
Returns codeFileContent, which holds the line-wise content of the source code files specified by every node.
getCodeFileContentForKey(String) - Method in class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
Returns line-wise content of the specified file. codeFileContent is gradually added to: when the node given to getHTMLforNode() specifies a source code file that is not in codeFileContent yet.
getComparator(String) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
Returns the Comparator that is currently set for the given keyword.
getComparator(int) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
Returns the Comparator that is currently set for the given keyword.
getComparatorDistances() - Method in class de.unibi.citec.tcs.alignment.Operation
Returns the local costs given by the Comparators specified for this Alignment to align the left Node in this Operation with the right Node (or deleting, inserting, skipping nodes respectively).
getCompareMatrix() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getCompressor() - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
 
getContent(String) - Method in class de.unibi.citec.tcs.alignment.visualization.ExternalContent
Returns the external content for a specific keyword.
getContent(String, int) - Method in class de.unibi.citec.tcs.alignment.visualization.ExternalContent
Returns the external content for a specific keyword and index.
getCostMatrix() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
Returns the ReplacementCosts object that defines the explicit cost matrix for replacements between the symbols in the given alphabet.
getCostMatrix() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Returns the cost matrix itself.
getDefaultComparator() - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
This returns a valid Comparator for this KeywordSpecification.
getDelCosts() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getDeleteComparison() - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
getDeletionCost(String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
getDeletionCost() - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
Returns the (constant) cost for deleting a value.
getDeletionCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Returns all deletion costs without any other costs.
getDeletionMatrix() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getDelLocal() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getDelLocal() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
 
getDelProb() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getDelSoftDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getDerivative() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
 
getDifference(AlignmentPath) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Returns the difference at each operation of the given AlignmentPath.
getDoCalculation() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
Please refer to the corresponding setter method for more information.
getDp_tables() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getEntryClass() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
Returns the class of matrix entries.
getExtensions(AlignmentPath) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Returns the sequence extensions modelled by this AlignmentPath.
getFiles() - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
Returns the files map.
getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
 
getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractSpecialHTMLTransformer
Transforms the given node into HTML content for the visualization.
getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.HTImageFromPath
Takes an image file from the given node and generates a corresponding HTML representation.
getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
Takes some code positions from the given node and extracts the corresponding string from a file specified by 'SourceCodeFile' in the node.
getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.PartStringFromFileExternalContent
 
getHTMLforNode(Node) - Method in interface de.unibi.citec.tcs.alignment.visualization.SpecialHTMLTransformer
Transforms the given node into HTML content for the visualization.
getI() - Method in class de.unibi.citec.tcs.alignment.MatrixCoordinate
 
getI() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
 
getI() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
 
getInsCosts() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getInsertComparison() - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
getInsertionCost(String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
getInsertionCost() - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
Returns the (constant) cost for inserting a value.
getInsertionCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Returns all insertion costs without any other costs.
getInsertionMatrix() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getInsLocal() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getInsLocal() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
 
getInsProb() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getInsSoftDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getJ() - Method in class de.unibi.citec.tcs.alignment.MatrixCoordinate
 
getJ() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
 
getJ() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
 
getKey() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
 
getKeyword(int) - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
Returns the keyword for the given index.
getKeyword() - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
Returns the keyword.
getKeyword() - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractSpecialHTMLTransformer
Returns the keyword that serves as column header for the visualization.
getKeyword() - Method in class de.unibi.citec.tcs.alignment.visualization.PartStringFromFileExternalContent
 
getKeyword() - Method in interface de.unibi.citec.tcs.alignment.visualization.SpecialHTMLTransformer
Returns the keyword that serves as column header for the visualization.
getKeywordIndex(String) - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
Returns the index of the given keyword.
getKeywords() - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
Returns the keywords that are mapped.
getKeywordSpecification(String) - Method in class de.unibi.citec.tcs.alignment.sequence.NodeSpecification
Returns the specification for the given keyword.
getKeywordSpecification(int) - Method in class de.unibi.citec.tcs.alignment.sequence.NodeSpecification
Returns the specification for the given keyword.
getLastAlignmentMatrix() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
The last matrix that was calculated using this algorithm.
getLastDTWMatrix() - Method in class de.unibi.citec.tcs.alignment.AbstractStrictDTWAlgorithm
This returns the dynamic programming matrix that was calculated in the last call of calculateAlignment.
getLeft() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
 
getLeft() - Method in class de.unibi.citec.tcs.alignment.Operation
 
getLeft() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
Returns the left input sequence.
getLeftSequence() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getLength() - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialKeywordSpecification
The length all vectors for this keyword have to have.
getM() - Method in class de.unibi.citec.tcs.alignment.MatrixCoordinate
 
getMatchCost() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
 
getMinMiddleSkips() - Method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
The minimum number of skips that have to be done in the middle of an alignment.
getMinMiddleSkips() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getMismatchCost() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
 
getNodes() - Method in class de.unibi.citec.tcs.alignment.sequence.Sequence
Returns the actual list of nodes.
getNodeSpecification() - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
 
getNodeSpecificiation() - Method in class de.unibi.citec.tcs.alignment.sequence.Sequence
Returns the NodeSpecification all Nodes in this sequence belong to.
getNormalizer() - Method in class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
Please refer to the corresponding setter method for more information.
getNormalizer() - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
Please refer to the corresponding setter method for more information.
getNumberOfComparisonParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
Implementing classes should return the number of (derivative-relevant) parameters used for the compare-function.
getNumberOfComparisonParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
Implementing classes should return the number of (derivative-relevant) parameters used for the compare-function.
getNumberOfComparisonParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
Implementing classes should return the number of (derivative-relevant) parameters used for the compare-function.
getNumberOfComparisonParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
Implementing classes should return the number of (derivative-relevant) parameters used for the compare-function.
getNumberOfComparisonParameters() - Method in class de.unibi.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.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
Implementing classes should return the number of (derivative-relevant) parameters used for the compare-function.
getNumberOfParameters() - Method in interface de.unibi.citec.tcs.alignment.comparators.DerivableComparator
This shall return the number of parameters of this comparator.
getNumberOfParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
 
getNumberOfParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
 
getNumberOfParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This shall return the number of parameters of this comparator.
getNumberOfThreads() - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
Please refer to the corresponding setter method for more information.
getNumberOfThreads() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
Please refer to the corresponding setter method for more information.
getOperations() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
 
getOriginalIndex(int) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
This is semantically equivalent to getNodeSpecification().getKeywordIndex(getKeyword(index)) but this is preprocessed here for better performance.
getParameterIndex() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
 
getPath() - Method in class de.unibi.citec.tcs.alignment.Operation
 
getPathLimit() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
Returns the the number of paths that shall be sampled.
getPathLimit() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
Please refer to the corresponding setter-method for more information.
getPathLimit() - Method in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
Please refer to the corresponding setter method for more calculation.
getPathMatrix() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
This is the dynamic programming matrix calculated by a SoftAlignmentAlgorithm.
getPaths(double) - Method in class de.unibi.citec.tcs.alignment.PathMap
Returns all paths with the given score.
getPredecessor() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
 
getRepCosts() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getReplacementCost(String, String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
getReplacementCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Returns the whole matrix of replacement costs without gap and skip costs.
getRepLocal() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getRepLocal() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
 
getRepProb() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getRepSoftDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getResultClass() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This method shall return the class of the alignment result.
getResultClass() - Method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
This method shall return the class of the alignment result.
getResultClass() - Method in class de.unibi.citec.tcs.alignment.AbstractStrictDTWAlgorithm
This method shall return the class of the alignment result.
getResultClass() - Method in interface de.unibi.citec.tcs.alignment.AlignmentAlgorithm
This method shall return the class of the alignment result.
getResultClass() - Method in interface de.unibi.citec.tcs.alignment.comparators.DerivableComparator
Returns the class of the intuitive format of the derivatives for all parameters of this comparator.
getResultClass() - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
 
getResultClass() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
 
getResultClass() - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
 
getResultClass() - Method in class de.unibi.citec.tcs.alignment.DynamicTimeWarpingAlgorithm
 
getResultMatrix() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
This returns the matrix of results if the calculation is done or null if it has not finished yet.
getRight() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
 
getRight() - Method in class de.unibi.citec.tcs.alignment.Operation
 
getRight() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
Returns the right input sequence.
getRightSequence() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getScore() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
 
getScore() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm.ScoreEntry
 
getScore() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getScore() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
Returns the soft alignment score between the two input sequences, normalized between 0 and 1, where 0 means a perfect similarity and 1 a absolute dissimilarity.
getScore() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
 
getScore() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm.ScoreEntry
 
getScore() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
 
getScoreMatrix() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
This method will only work if the Result class is Double.
getScores() - Method in class de.unibi.citec.tcs.alignment.PathMap
Get all scores for which paths exist within this map.
getSequence() - Method in class de.unibi.citec.tcs.alignment.sequence.Node
Returns the sequence this node belongs to.
getSequences() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
 
getSigma() - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
 
getSimilarityMatrix() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
This is the dynamic programming matrix calculated by a DynamicTimeWarpingAlgorithm.
getSimilarityScore() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
Returns the softDTW score between the two input sequences.
getSize() - Method in class de.unibi.citec.tcs.alignment.PathMap
Returns the number of paths stored in this map.
getSkipDeleteComparison() - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
getSkipDeletionCost(String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
getSkipDeletionCost() - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
Returns the (constant) cost for deleting a value using a skip.
getSkipDeletionCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Returns all skip deletion costs without any other costs.
getSkipDeletionMatrix() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getSkipFactor() - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
Returns the cost factor for skipDeletions and skipInsertions for a dynamic comparison.
getSkipInsertComparison() - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
getSkipInsertionCost(String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
getSkipInsertionCost() - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
Returns the (constant) cost for inserting a value using a skip.
getSkipInsertionCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Returns all skip insertion costs without any other costs.
getSkipInsertionMatrix() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getSoftmin() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
getSpecification() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This should return the specification that is used for this Algorithm.
getSpecification() - Method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
This should return the specification that is used for this Algorithm.
getSpecification() - Method in class de.unibi.citec.tcs.alignment.AbstractStrictDTWAlgorithm
This should return the specification that is used for this Algorithm.
getSpecification() - Method in interface de.unibi.citec.tcs.alignment.AlignmentAlgorithm
This should return the specification that is used for this Algorithm.
getSpecification() - Method in class de.unibi.citec.tcs.alignment.DynamicTimeWarpingAlgorithm
 
getSpecification() - Method in class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
getSpecification() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
Returns the AlignmentSpecification that was basis for this Alignment.
getSpecificationClass() - Method in enum de.unibi.citec.tcs.alignment.sequence.ValueType
Returns the corresponding specification class for this ValueType.
getSpecificaton() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
 
getSpecificaton() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
Returns the AlignmentSpecification that was basis for this Alignment.
getString() - Method in class de.unibi.citec.tcs.alignment.sequence.StringValue
Returns the actual string.
getSymbol(int) - Method in class de.unibi.citec.tcs.alignment.sequence.Alphabet
This is equivalent to "getKeyword"
getSymbol() - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
Returns this actual symbol.
getSymbolIndex(String) - Method in class de.unibi.citec.tcs.alignment.sequence.Alphabet
This is equivalent to "getKeywordIndex"
getSymbols() - Method in class de.unibi.citec.tcs.alignment.sequence.Alphabet
This is equivalent to "getKeywords"
getType() - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
getType() - Method in interface de.unibi.citec.tcs.alignment.comparators.Comparator
 
getType() - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
 
getType() - Method in class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
getType() - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
getType() - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
getType() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
getType() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
getType() - Method in class de.unibi.citec.tcs.alignment.Operation
 
getType() - Method in class de.unibi.citec.tcs.alignment.sequence.AbstractValue
Returns the type of this value.
getType() - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
Returns the specified type for that keyword.
getType() - Method in interface de.unibi.citec.tcs.alignment.sequence.Value
Returns the type of this value.
getValue() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
 
getValue() - Method in class de.unibi.citec.tcs.alignment.Counter
 
getValue(String) - Method in class de.unibi.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.unibi.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.unibi.citec.tcs.alignment.sequence.ValueType
The corresponding class of this ValueType.
getVector() - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
Returns the actual vector.
getWeightedLocalCost() - Method in class de.unibi.citec.tcs.alignment.Operation
 
getWeighting() - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
Returns the current keyword weighting.
getWeighting() - Method in class de.unibi.citec.tcs.alignment.PathMap
Returns the weighting that is used during derivative calculation.
getWeightThreshold() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
 
getWeightThreshold() - Method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
 
getWeightThreshold() - Method in class de.unibi.citec.tcs.alignment.AbstractStrictDTWAlgorithm
 
getX() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
Returns the first input sequence.
getY() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
Returns the second input sequence.

H

hashCode() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
hashCode() - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
hashCode() - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
hashCode() - Method in class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
hashCode() - Method in class de.unibi.citec.tcs.alignment.comparators.ExponentialNormalizer
hashCode() - Method in class de.unibi.citec.tcs.alignment.comparators.HyperbolicNormalizer
hashCode() - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
hashCode() - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
hashCode() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
hashCode() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
hashCode() - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
hashCode() - Method in class de.unibi.citec.tcs.alignment.MatrixCoordinate
The HashCode given here defines the MatrixCoordinate uniquely as i*m + j, giving an bijective mapping of HashCodes to actual MatrixCoordinates.
hashCode() - Method in class de.unibi.citec.tcs.alignment.Operation
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.AbstractValue
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.Node
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.NodeSpecification
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.Sequence
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.StringValue
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialKeywordSpecification
hashCode() - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
hashCode() - Method in class de.unibi.citec.tcs.alignment.SparseMatrix
hasKeyword(String) - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
Returns true if and only if this keyword is contained in the mapping.
hasNext() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.EmptySparseLocalEntry
hasNext() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FixedSparseLocalDerivative
hasNext() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.TrivialSparseLocalDerivative
hasSymbol(String) - Method in class de.unibi.citec.tcs.alignment.sequence.Alphabet
This is equivalent to "hasKeyword".
highestScore() - Method in class de.unibi.citec.tcs.alignment.PathMap
Returns the highest/worst score stored in this map.
HTImageFromPath - Class in de.unibi.citec.tcs.alignment.visualization
 
HTImageFromPath(String) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTImageFromPath
Attention: when using this constructor, you have to call setFiles() manually.
HTImageFromPath(String, String[]) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTImageFromPath
Initializes given files or folders.
HTImageFromPath(String, String) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTImageFromPath
Initializes given folder.
HTImageFromPath(String, File[]) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTImageFromPath
Initializes given files or folders.
HTImageFromPath(String, File) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTImageFromPath
Initializes given folder.
HTPartStringFromPath - Class in de.unibi.citec.tcs.alignment.visualization
 
HTPartStringFromPath(String) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
Attention: when using this constructor, you have to call setFiles() or setCodeFileContent() manually.
HTPartStringFromPath(String, String[]) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
Initializes given files or folders.
HTPartStringFromPath(String, String) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
Initializes given folder.
HTPartStringFromPath(String, File[]) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
Initializes given files or folders.
HTPartStringFromPath(String, File) - Constructor for class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
Initializes given folder.
HyperbolicNormalizer - Class in de.unibi.citec.tcs.alignment.comparators
This normalizes by using the function 1 - 1/(d+1).
HyperbolicNormalizer() - Constructor for class de.unibi.citec.tcs.alignment.comparators.HyperbolicNormalizer
 

I

IMAGE_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 
inc() - Method in class de.unibi.citec.tcs.alignment.Counter
 
IndexedStochasticPriorityQueue<K extends Comparable<K>,V> - Class in de.unibi.citec.tcs.alignment
This is a helper class, which actually extends the TreeMap to implement a PriorityQueue that is able to poll the minimum as well as the maximum in constanst time.
IndexedStochasticPriorityQueue() - Constructor for class de.unibi.citec.tcs.alignment.IndexedStochasticPriorityQueue
 
IndexingScheme - Class in de.unibi.citec.tcs.alignment.sequence
This serves as an abstract superclass for classes that define an indexing scheme for keywords.
IndexingScheme(HashMap<String, Integer>) - Constructor for class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
Constructs an IndexingScheme from a mapping of strings to indices.
IndexingScheme(String[]) - Constructor for class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
Constructs an IndexingScheme from a mapping of indices to strings.
IndexingScheme(String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
Constructor for symbols either encoded as single characters without delimiter or as strings with | as delimiter.
insert(V) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
This should be called during an alignment to retrieve the costs for an insertion of value b into the first sequence.
insert(X) - Method in interface de.unibi.citec.tcs.alignment.comparators.GapComparator
This should be called during an alignment to retrieve the costs for an insertion of value b into the first sequence.
insert(SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
This should be called during an alignment to retrieve the costs for an insertion of value b into the first sequence.
insert(V) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This should be called during an alignment to retrieve the costs for an insertion of value b into the first sequence.
isDynamic() - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
Returns true if and only if this comparator will use a dynamic method to determine deletion, insertion and skip costs.
isFinished() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
 
isGapAlignmentMatrix() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
isIgnoreExceptions() - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
If this is set to true exceptions in single threads are ignored.
isIgnoreExceptions() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
If this is set to true exceptions in single threads are ignored.
isLocalAlignmentMatrix() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
isSymmetric() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
Please refer to the corresponding setter method for more information.
isValidWeighting(double[]) - Static method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
This checks whether the given weighting is a valid one.
isVerbose() - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
If verbose is set to true the ParallelProcessingEngine will give information about the current state of the calculation.
isVerbose() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
If verbose is set to true the ParallelProcessingEngine will give information about the current state of the calculation.
iterator() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.EmptySparseLocalEntry
iterator() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FixedSparseLocalDerivative
iterator() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.TrivialSparseLocalDerivative

K

Keywords - Class in de.unibi.citec.tcs.alignment.visualization
 
Keywords() - Constructor for class de.unibi.citec.tcs.alignment.visualization.Keywords
 
KeywordSpecification - Class in de.unibi.citec.tcs.alignment.sequence
This specifies a keyword via its name and the type of its values.
KeywordSpecification(String, ValueType) - Constructor for class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
Sets up a KeywordSpecification that defines a type for the given keyword.

L

L1NormComparator - Class in de.unibi.citec.tcs.alignment.comparators
Compares vectors using the L1-Norm.
L1NormComparator(int) - Constructor for class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(Normalizer, int) - Constructor for class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(int, double) - Constructor for class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(Normalizer, int, double) - Constructor for class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(VectorialValue, VectorialValue, VectorialValue, VectorialValue) - Constructor for class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
 
L1NormComparator(Normalizer, VectorialValue, VectorialValue, VectorialValue, VectorialValue) - Constructor for class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
 
LocalAlignmentAlgorithm<R> - Interface in de.unibi.citec.tcs.alignment
This is an interface for GapAlignmentAlgorithms that also use skips (SkipDeletion, SkipInsertion) and in that way are local distance measures.
lowestScore() - Method in class de.unibi.citec.tcs.alignment.PathMap
Returns the lowest/best score stored in this map.

M

mapToDoubleVector(Object) - Static method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
Tries to convert an object to a double vector.
MatrixCoordinate - Class in de.unibi.citec.tcs.alignment
Identifies a position in a two-dimensional matrix.
MatrixCoordinate(int, int, int) - Constructor for class de.unibi.citec.tcs.alignment.MatrixCoordinate
 
MISMATCHDEFAULT - Static variable in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 

N

NAME_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 
NCDComparator - Class in de.unibi.citec.tcs.alignment.comparators
This compares strings using normalized compression distance.
NCDComparator() - Constructor for class de.unibi.citec.tcs.alignment.comparators.NCDComparator
 
NCDComparator.CompressorType - Enum in de.unibi.citec.tcs.alignment.comparators
This class contains all possible CompressorTypes for this NCD implementation.
next() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.EmptySparseLocalEntry
next() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FixedSparseLocalDerivative
next() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.TrivialSparseLocalDerivative
Node - Class in de.unibi.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.unibi.citec.tcs.alignment.sequence.Node
 
NodeSpecification - Class in de.unibi.citec.tcs.alignment.sequence
This specifies the contents of the nodes in a given sequence.
NodeSpecification(KeywordSpecification[]) - Constructor for class de.unibi.citec.tcs.alignment.sequence.NodeSpecification
 
normalize(double) - Method in class de.unibi.citec.tcs.alignment.comparators.ExponentialNormalizer
normalize(double) - Method in class de.unibi.citec.tcs.alignment.comparators.HyperbolicNormalizer
normalize(double) - Method in interface de.unibi.citec.tcs.alignment.comparators.Normalizer
 
Normalizer - Interface in de.unibi.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.
NUMBER_OF_EDGES_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 

O

Operation - Class in de.unibi.citec.tcs.alignment
This defines an applied alignment operation.
Operation(Node, Node, OperationType, AlignmentPath) - Constructor for class de.unibi.citec.tcs.alignment.Operation
This constructs an Operation within an AlignmentPath.
OperationType - Enum in de.unibi.citec.tcs.alignment
This defines the possible types of operations that may be used in an alignment within this Toolbox.

P

ParallelDerivativeEngine - Class in de.unibi.citec.tcs.alignment
This allows parallel processing of derivative calculations.
ParallelDerivativeEngine(AlignmentDerivativeAlgorithm[]) - Constructor for class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm and the given Sequences.
ParallelDerivativeEngine(AlignmentDerivativeAlgorithm[][]) - Constructor for class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
 
ParallelProcessingEngine<R> - Class in de.unibi.citec.tcs.alignment
This allows parallel processing of alignment calculations.
ParallelProcessingEngine(AlignmentAlgorithm<R>, Sequence[]) - Constructor for class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm and the given Sequences.
PartStringFromFileExternalContent - Class in de.unibi.citec.tcs.alignment.visualization
 
PartStringFromFileExternalContent(String, String[]) - Constructor for class de.unibi.citec.tcs.alignment.visualization.PartStringFromFileExternalContent
 
PartStringFromFileExternalContent(String, String) - Constructor for class de.unibi.citec.tcs.alignment.visualization.PartStringFromFileExternalContent
 
PartStringFromFileExternalContent(String, File[]) - Constructor for class de.unibi.citec.tcs.alignment.visualization.PartStringFromFileExternalContent
 
PartStringFromFileExternalContent(String, File) - Constructor for class de.unibi.citec.tcs.alignment.visualization.PartStringFromFileExternalContent
 
PathList - Class in de.unibi.citec.tcs.alignment
This is a list-based datastructure accumulating multiple AlignmentPaths.
PathList() - Constructor for class de.unibi.citec.tcs.alignment.PathList
 
PathMap - Class in de.unibi.citec.tcs.alignment
This is a TreeMap-based datastructure implementing a mapping from scores to AlignmentPaths.
PathMap() - Constructor for class de.unibi.citec.tcs.alignment.PathMap
 
pollFirst() - Method in class de.unibi.citec.tcs.alignment.IndexedStochasticPriorityQueue
Polls the value associated with the minimum key.
pollLast() - Method in class de.unibi.citec.tcs.alignment.IndexedStochasticPriorityQueue
Polls the value associated with the maximum key.
put(K, V) - Method in class de.unibi.citec.tcs.alignment.IndexedStochasticPriorityQueue
 
put(AlignmentPath) - Method in class de.unibi.citec.tcs.alignment.PathMap
Adds a new AlignmentPath to this map.

R

RandomSequenceGenerator - Class in de.unibi.citec.tcs.alignment.wrappers
This class is more for demonstration purposes and creates random sequences according to given input parameters.
RandomSequenceGenerator() - Constructor for class de.unibi.citec.tcs.alignment.wrappers.RandomSequenceGenerator
 
readFile(File) - Static method in class de.unibi.citec.tcs.alignment.visualization.Utils
Reads a File and returns its content as a list of Strings.
readFileFromPath(String) - Static method in class de.unibi.citec.tcs.alignment.visualization.Utils
Finds a file at its paths, reads it in and returns its content as a list of Strings.
realValuesToRgbColors(Set<Double>, double, double) - Static method in class de.unibi.citec.tcs.alignment.visualization.Utils
Calculates a coloring scheme from dark green to yellow from given values.
remove() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.EmptySparseLocalEntry
remove() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FixedSparseLocalDerivative
remove() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.TrivialSparseLocalDerivative
removeValues(double) - Method in class de.unibi.citec.tcs.alignment.PathMap
Removes all AlignmentPaths with the given score from the map and returns them.
ReplacementComparator - Class in de.unibi.citec.tcs.alignment.comparators
This comparator defines explicit replacement (and deletion/insertion) costs for comparison of symbolic values.
ReplacementComparator() - Constructor for class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
 
ReplacementComparator(ReplacementCosts) - Constructor for class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
 
ReplacementCosts - Class in de.unibi.citec.tcs.alignment.comparators
This is a matrix of parameters specifying costs to replace one symbol of an alphabet with another one.
ReplacementCosts(Alphabet, boolean, boolean) - Constructor for class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Initializes an empty replacement score matrix with sensible defaults: The diagonal is set to 0 (it costs nothing to replace a symbol by itself), every other replacement is set to MISMATCHDEFAULT, gap costs are set to GAPDEFAULT and skip costs to SKIPDEFAULT.
ReplacementCosts(Alphabet, double[][]) - Constructor for class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
rgbColorsForAlignments(AlignmentPath[][]) - Static method in class de.unibi.citec.tcs.alignment.visualization.Utils
Calculates a color scheme for all alignment scores (for form.html).
rgbColorsForKeys(AlignmentPath[][]) - Static method in class de.unibi.citec.tcs.alignment.visualization.Utils
Calculates a color scheme for all keys over all alignments.
rgbColorsForOperations(ArrayList<Operation>) - Static method in class de.unibi.citec.tcs.alignment.visualization.Utils
Calculates a color scheme for all operation scores in an alignment.

S

ScoreBasedWeighting - Enum in de.unibi.citec.tcs.alignment
This is a helper class to enable users to weight a collection of scores based on different schemes specified below.
Sequence - Class in de.unibi.citec.tcs.alignment.sequence
Usually a sequence for alignments is defined as a sequence of symbols.
Sequence(NodeSpecification) - Constructor for class de.unibi.citec.tcs.alignment.sequence.Sequence
Sets up an empty sequence with the given NodeSpecification as basis.
Sequence(String) - Constructor for class de.unibi.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.unibi.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.
set(int, int, X) - Method in class de.unibi.citec.tcs.alignment.SparseMatrix
Sets the value at the given position in the matrix.
setAlpha(double) - Method in class de.unibi.citec.tcs.alignment.comparators.HyperbolicNormalizer
 
setApproxThreshold(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
Sets the threshold for which exponents within the softmin function will be disregarded.
setApproxThreshold(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
Sets the threshold for which exponents within the softmin function will be disregarded.
setApproxThreshold(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
For more information on the ApproxThreshold have a look at the Softmin class.
setApproxThreshold(double) - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentFullAlgorithm
For more information on the ApproxThreshold have a look at the Softmin class.
setApproxThreshold(double) - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentScoreAlgorithm
For more information on the ApproxThreshold have a look at the Softmin class.
setBeta(double) - Method in class de.unibi.citec.tcs.alignment.comparators.ExponentialNormalizer
 
setBeta(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
 
setBeta(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
 
setBeta(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
 
setBeta(double) - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentFullAlgorithm
 
setBeta(double) - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentScoreAlgorithm
 
setCodeFileContent(Map<String, ArrayList<String>>) - Method in class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
Sets codeFileContent, which holds the line-wise content of the source code files specified by every node.
setComparator(String, Comparator) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
Sets the comparator for a given keyword.
setComparator(int, Comparator) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
Sets the comparator for a given keyword.
setComparatorDistances(double[]) - Method in class de.unibi.citec.tcs.alignment.Operation
Sets the local costs given by the Comparators specified for this Alignment to align the left Node in this Operation with the right Node (or deleting, inserting, skipping nodes respectively).
setCompressor(NCDComparator.CompressorType) - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
 
setCostMatrix(ReplacementCosts) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
Sets the ReplacementCosts that shall be used within this Comparator.
setCostMatrix(double[][]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Sets the cost matrix itself.
setDelCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setDeleteComparison(V) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
setDeletionCost(String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
setDeletionCost(double) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
Sets the (constant) cost for deleting a value.
setDeletionCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Sets all deletion costs without any other costs.
setDelLocal(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setDelProb(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setDelSoftDerivative(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setDoCalculation(boolean[][]) - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
This enables a user to specifically set which pairwise similarity calculations should be done and which should not be done.
setDynamic(boolean) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
Set to true if and only if this comparator shall use a dynamic method to determine deletion, insertion and skip costs.
setFiles(Map<String, File>) - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
Sets the files map directly.
setIgnoreExceptions(boolean) - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
If this is set to true exceptions in single threads are ignored.
setIgnoreExceptions(boolean) - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
If this is set to true exceptions in single threads are ignored.
setInsCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setInsertComparison(V) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
setInsertionCost(String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
setInsertionCost(double) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
Sets the (constant) cost for inserting a value.
setInsertionCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Sets all insertion costs without any other costs.
setInsLocal(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setInsProb(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setInsSoftDerivative(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setMatchCost(double) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
 
setMinMiddleSkips(int) - Method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
The minimum number of skips that have to be done in the middle of an alignment.
setMismatchCost(double) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
 
setNormalizer(Normalizer) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
The euclidian distance per default is bound by 0 but has no upper bound.
setNormalizer(Normalizer) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
The L1-norm per default is bound by 0 but has no upper bound.
setNumberOfThreads(int) - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
Sets the number of threads that are used.
setNumberOfThreads(int) - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
Sets the number of threads that are used.
setPathLimit(int) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
This sets the number of paths that shall be sampled.
setPathLimit(int) - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
The total number of co-optimal alignments can be very huge as multiple co-optimal operations lead to a combinatorial explosion of possible alignments.
setPathLimit(int) - Method in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
This sets the k that gives the StrictKPathAlgorithm its name: The number of returned AlignmentPaths is limited to the k best alignments.
setRepCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setReplacementCost(String, String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
setReplacementCosts(double[][]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Sets the whole matrix of replacement costs without gap and skip costs.
setRepLocal(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setRepProb(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setRepSoftDerivative(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setSkipDeleteComparison(V) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
setSkipDeletionCost(String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
setSkipDeletionCost(double) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
Sets the (constant) cost for deleting a value using a skip.
setSkipDeletionCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Sets all skip deletion costs without any other costs.
setSkipFactor(double) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
Sets the cost factor for skipDeletions and skipInsertions for a dynamic comparison.
setSkipInsertComparison(V) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
 
setSkipInsertionCost(String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
setSkipInsertionCost(double) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
Sets the (constant) cost for inserting a value using a skip.
setSkipInsertionCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
Sets all skip insertion costs without any other costs.
setSoftmin(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
setString(String) - Method in class de.unibi.citec.tcs.alignment.sequence.StringValue
 
setSymbol(String) - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
Sets the actual symbol.
setSymmetric(boolean) - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
If this is set to true it is assumed that the desired result of the alignment is symmetric, meaning that the alignment between the sequences i and j is equal to the alignment between j and i.
setUpSpecification(Sequence[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
Sets up a default AlignmentSpecification for the simple StringEditDistance problem.
setUpSpecification(Sequence[], double, double, double) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
Sets up an AlignmentSpecification for the simple StringEditDistance problem.
setUpSpecification(Sequence[], double[][]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
Sets up an AlignmentSpecification for the simple StringEditDistance problem.
setUpSpecification(Sequence[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], GapComparator<VectorialValue>) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], GapComparator[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], double[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], GapComparator<VectorialValue>, double[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setUpSpecification(Sequence[], GapComparator[], double[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Sets up an AlignmentSpecification for an array of vectorial sequences.
setValue(Double) - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
 
setValue(String, Value) - Method in class de.unibi.citec.tcs.alignment.sequence.Node
Sets the value for the given keyword.
setValue(int, Value) - Method in class de.unibi.citec.tcs.alignment.sequence.Node
Sets the value for the given keyword.
setVector(double[]) - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
Sets the actual vector.
setVector(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
Sets the actual vector.
setVerbose(boolean) - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
If verbose is set to true the ParallelProcessingEngine will give information about the current state of the calculation.
setVerbose(boolean) - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
If verbose is set to true the ParallelProcessingEngine will give information about the current state of the calculation.
setWeighting(double[]) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
This sets the current weighting of keywords.
setWeighting(ScoreBasedWeighting) - Method in class de.unibi.citec.tcs.alignment.PathMap
Sets the weighting that is used during derivative calculation.
setWeightThreshold(double) - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
Set a weight threshold (between 0 and 1) that determines which keywords should be ignored during calculation because their weight is negligible.
setWeightThreshold(double) - Method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
Set a weight threshold (between 0 and 1) that determines which keywords should be ignored during calculation because their weight is negligible.
setWeightThreshold(double) - Method in class de.unibi.citec.tcs.alignment.AbstractStrictDTWAlgorithm
Set a weight threshold (between 0 and 1) that determines which keywords should be ignored during calculation because their weight is negligible.
SHOW_STEPS - Static variable in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
 
SHOW_STEPS - Static variable in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
 
size() - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
Returns the number of mapped keywords.
SkipComparator<X extends Value> - Interface in de.unibi.citec.tcs.alignment.comparators
This further specifies the AlignmentComparator to include skips.
SKIPDEFAULT - Static variable in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
 
skipDelete(V) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
This should be called during an alignment to retrieve the costs for a skip deletion of value a from the first sequence.
skipDelete(SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
This should be called during an alignment to retrieve the costs for a skip deletion of value a from the first sequence.
skipDelete(X) - Method in interface de.unibi.citec.tcs.alignment.comparators.SkipComparator
This should be called during an alignment to retrieve the costs for a skip deletion of value a from the first sequence.
skipDelete(V) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This should be called during an alignment to retrieve the costs for a skip deletion of value a from the first sequence.
SkipExtendedComparator<V extends Value> - Class in de.unibi.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.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
 
skipInsert(V) - Method in class de.unibi.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
This should be called during an alignment to retrieve the costs for a skip insertion of value b into the first sequence.
skipInsert(SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
This should be called during an alignment to retrieve the costs for a skip insertion of value b into the first sequence.
skipInsert(X) - Method in interface de.unibi.citec.tcs.alignment.comparators.SkipComparator
This should be called during an alignment to retrieve the costs for a skip insertion of value b into the first sequence.
skipInsert(V) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This should be called during an alignment to retrieve the costs for a skip insertion of value b into the first sequence.
SoftAlignmentFullAlgorithm - Class in de.unibi.citec.tcs.alignment
This calculates the soft (global) alignment of two sequences similarly to the Needleman-Wunsch-Algorithm.
SoftAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
This sets up an AlignmentAlgorithm instance according to the given specification.
SoftAlignmentSamplingAlgorithm - Class in de.unibi.citec.tcs.alignment
This calculates the soft (global) alignment of two sequences similarly to the Needleman-Wunsch-Algorithm.
SoftAlignmentSamplingAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
This sets up an AlignmentAlgorithm instance according to the given specification.
SoftAlignmentScoreAlgorithm - Class in de.unibi.citec.tcs.alignment
This calculates the soft (global) alignment of two sequences similarly to the Needleman-Wunsch-Algorithm.
SoftAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
This sets up an AlignmentAlgorithm instance according to the given specification.
SoftAlignmentScoreAlgorithm.ScoreEntry - Class in de.unibi.citec.tcs.alignment
 
SoftAlignmentScoreAlgorithm.ScoreEntry(double) - Constructor for class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm.ScoreEntry
 
SoftDTWModel - Class in de.unibi.citec.tcs.alignment
storage unit for soft DTW alignment result, provides functions to calculate the soft DTW derivatives based on the stored soft alignment
SoftDTWModel(AlignmentSpecification, Sequence, Sequence, double[][]) - Constructor for class de.unibi.citec.tcs.alignment.SoftDTWModel
 
SoftLocalAlignmentFullAlgorithm - Class in de.unibi.citec.tcs.alignment
This implements a local affine alignment similar to Smith-Waterman and Gotoh.
SoftLocalAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.SoftLocalAlignmentFullAlgorithm
 
SoftLocalAlignmentScoreAlgorithm - Class in de.unibi.citec.tcs.alignment
This implements a local affine alignment similar to Smith-Waterman and Gotoh.
SoftLocalAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.SoftLocalAlignmentScoreAlgorithm
 
SoftLocalPathModel - Class in de.unibi.citec.tcs.alignment
This is basically a storage for the DTW matrix of the SoftLocalAlignmentAlgorithm.
SoftLocalPathModel(double, AlignmentSpecification, int, double, EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence, double[][]>, double[][], double[], double[], double[], double[], Sequence, Sequence) - Constructor for class de.unibi.citec.tcs.alignment.SoftLocalPathModel
 
Softmin - Class in de.unibi.citec.tcs.alignment
This implements utility functions for the softmin function.
Softmin() - Constructor for class de.unibi.citec.tcs.alignment.Softmin
 
softmin(double, double[]) - Static method in class de.unibi.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.unibi.citec.tcs.alignment.Softmin
This calculates softmin for the given input and the given value of beta.
SoftPathModel - Class in de.unibi.citec.tcs.alignment
This is the soft pendant to the AlignmentPath.
SoftPathModel(AlignmentSpecification, Sequence, Sequence, double, double, SoftPathModel.SoftMatrixEntry[][]) - Constructor for class de.unibi.citec.tcs.alignment.SoftPathModel
 
SoftPathModel.SoftMatrixEntry - Class in de.unibi.citec.tcs.alignment
 
SoftPathModel.SoftMatrixEntry() - Constructor for class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
 
SOURCE_CODE_FILE_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 
SOURCE_CODE_PART_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 
sparseComparisonDerivative(StringValue, StringValue) - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
This should implement the local derivative calculation in case of comparisons.
sparseComparisonDerivative(VectorialValue, VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclideanComparator
This should implement the local derivative calculation in case of comparisons.
sparseComparisonDerivative(VectorialValue, VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
This should implement the local derivative calculation in case of comparisons.
sparseComparisonDerivative(StringValue, StringValue) - Method in class de.unibi.citec.tcs.alignment.comparators.NCDComparator
This should implement the local derivative calculation in case of comparisons.
sparseComparisonDerivative(V, V) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This should implement the local derivative calculation in case of comparisons.
sparseComparisonDerivative(SymbolicValue, SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
This should implement the local derivative calculation in case of comparisons.
SparseDerivableComparator<X extends Value,Y> - Interface in de.unibi.citec.tcs.alignment.comparators
Some derivable comparators have the special property that in each alignment step only a small subset of parameters is needed.
SparseLocalDerivative - Interface in de.unibi.citec.tcs.alignment.comparators
This is an interface for classes that are able to hold sparse representations of a local derivative, where only for one or a few parameters the derivative is non-zero.
SparseLocalDerivative.EmptySparseLocalEntry - Class in de.unibi.citec.tcs.alignment.comparators
 
SparseLocalDerivative.EmptySparseLocalEntry() - Constructor for class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.EmptySparseLocalEntry
 
SparseLocalDerivative.FixedSparseLocalDerivative - Class in de.unibi.citec.tcs.alignment.comparators
This implements the SparseLocalDerivative interface for a fixed number of entries.
SparseLocalDerivative.FixedSparseLocalDerivative(int) - Constructor for class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FixedSparseLocalDerivative
 
SparseLocalDerivative.FlexibleSparseLocalDerivative - Class in de.unibi.citec.tcs.alignment.comparators
 
SparseLocalDerivative.FlexibleSparseLocalDerivative() - Constructor for class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FlexibleSparseLocalDerivative
 
SparseLocalDerivative.SparseDeriativeEntry - Class in de.unibi.citec.tcs.alignment.comparators
 
SparseLocalDerivative.SparseDeriativeEntry(int, double) - Constructor for class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
 
SparseLocalDerivative.TrivialSparseLocalDerivative - Class in de.unibi.citec.tcs.alignment.comparators
This is a representation with just one entry.
SparseLocalDerivative.TrivialSparseLocalDerivative() - Constructor for class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.TrivialSparseLocalDerivative
 
SparseMatrix<X> - Class in de.unibi.citec.tcs.alignment
This models a sparse matrix that does not have to be fully calculated.
SparseMatrix() - Constructor for class de.unibi.citec.tcs.alignment.SparseMatrix
 
SpecialHTMLTransformer - Interface in de.unibi.citec.tcs.alignment.visualization
Interface to transform some sequence into HTML code.
STDKEYWORD - Static variable in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
 
StrictAlignmentFullAlgorithm - Class in de.unibi.citec.tcs.alignment
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
StrictAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm
This sets up an AlignmentAlgorithm instance according to the given specification.
StrictAlignmentFullAlgorithm.FullMatrixEntry - Class in de.unibi.citec.tcs.alignment
 
StrictAlignmentFullAlgorithm.FullMatrixEntry(double, int, int, StrictAlignmentFullAlgorithm.FullMatrixEntry) - Constructor for class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
 
StrictAlignmentScoreAlgorithm - Class in de.unibi.citec.tcs.alignment
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
StrictAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
This sets up an AlignmentAlgorithm instance according to the given specification.
StrictAlignmentScoreAlgorithm.ScoreEntry - Class in de.unibi.citec.tcs.alignment
 
StrictAlignmentScoreAlgorithm.ScoreEntry(double) - Constructor for class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm.ScoreEntry
 
StrictAllOptimalAlgorithm - Class in de.unibi.citec.tcs.alignment
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
StrictAllOptimalAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
This sets up an AlignmentAlgorithm instance according to the given specification.
StrictAllOptimalAlgorithm.FullMatrixEntry - Class in de.unibi.citec.tcs.alignment
 
StrictAllOptimalAlgorithm.FullMatrixEntry(double, double, double, double, int, int) - Constructor for class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
 
StrictDTWFullAlgorithm - Class in de.unibi.citec.tcs.alignment
This is an implementation of the AbstractStrictDTWAlgorithm to calculate just one exemplary optimal DTW path.
StrictDTWFullAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictDTWFullAlgorithm
 
StrictDTWScoreAlgorithm - Class in de.unibi.citec.tcs.alignment
This is an implementation of the AbstractStrictDTWAlgorithm to calculate just the score.
StrictDTWScoreAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictDTWScoreAlgorithm
 
StrictKPathAlgorithm - Class in de.unibi.citec.tcs.alignment
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
StrictKPathAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
This sets up an AlignmentAlgorithm instance according to the given specification.
StrictLocalAlignmentFullAlgorithm - Class in de.unibi.citec.tcs.alignment
This implements a local affine alignment similar to Smith-Waterman and Gotoh.
StrictLocalAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictLocalAlignmentFullAlgorithm
 
StrictLocalAlignmentScoreAlgorithm - Class in de.unibi.citec.tcs.alignment
This implements a local affine alignment similar to Smith-Waterman and Gotoh.
StrictLocalAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictLocalAlignmentScoreAlgorithm
 
StringEditDistance - Class in de.unibi.citec.tcs.alignment.wrappers
This is a simple wrapper to support an easier interface for the simple StringEditDistance problem.
StringEditDistance() - Constructor for class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
 
StringKeywordSpecification - Class in de.unibi.citec.tcs.alignment.sequence
This specifies String keywords which are not especially restricted.
StringKeywordSpecification(String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.StringKeywordSpecification
 
StringValue - Class in de.unibi.citec.tcs.alignment.sequence
This value is supposed to represent strings that are not restricted to a certain alphabet.
StringValue() - Constructor for class de.unibi.citec.tcs.alignment.sequence.StringValue
 
StringValue(String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.StringValue
 
SymbolicKeywordSpecification - Class in de.unibi.citec.tcs.alignment.sequence
This specifies symbolic keywords by their alphabet.
SymbolicKeywordSpecification(Alphabet, String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
 
SymbolicValue - Class in de.unibi.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.unibi.citec.tcs.alignment.sequence.SymbolicValue
 
SymbolicValue(Alphabet, String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
 

T

toMatrix() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
This transforms the AlignmentPath to a matrix, mostly for visualization purposes.
toMatrix() - Method in class de.unibi.citec.tcs.alignment.PathList
This transforms the PathList to a matrix, mostly for visualization purposes.
toMatrix() - Method in class de.unibi.citec.tcs.alignment.PathMap
This transforms the PathMap to a matrix, mostly for visualization purposes.
toSequences(String[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
toSequences(Collection<String>) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
Transforms the given strings to the TCSAlignmentToolbox Sequence format.
toSequences(String[], Alphabet) - Static method in class de.unibi.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.unibi.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.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Transforms the given arrays to sequences.
toSequences(double[][][]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Transforms the given arrays to sequences.
toSequences(double[][][], String[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Transforms the given arrays to sequences.
toSequences(double[][][], String[], int[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
Transforms the given arrays to sequences.
toString() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
toString() - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
 
toString() - Method in class de.unibi.citec.tcs.alignment.MatrixCoordinate
toString() - Method in class de.unibi.citec.tcs.alignment.Operation
toString() - Method in class de.unibi.citec.tcs.alignment.sequence.Alphabet
toString() - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
 
toString() - Method in class de.unibi.citec.tcs.alignment.sequence.NodeSpecification
 
toString() - Method in class de.unibi.citec.tcs.alignment.sequence.Sequence
toString() - Method in class de.unibi.citec.tcs.alignment.sequence.StringValue
toString() - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
toString() - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
toString() - Method in class de.unibi.citec.tcs.alignment.SparseMatrix
transformToResult(X[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
This method should not be called from outside!
transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence, double[][]>, double[][], double[], double[], double[], double[], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm
This method should not be called from outside!
transformToResult(double[][], Sequence, Sequence) - Method in class de.unibi.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(double[]) - Method in interface de.unibi.citec.tcs.alignment.comparators.DerivableComparator
This method is supposed to construct the derivative for this comparator in an intuitive format given its vectorial form.
transformToResult(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
This method is supposed to construct the derivative for this comparator in an intuitive format given its vectorial form.
transformToResult(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
 
transformToResult(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.SkipExtendedComparator
This method is supposed to construct the derivative for this comparator in an intuitive format given its vectorial form.
transformToResult(SoftPathModel.SoftMatrixEntry[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
This method should not be called from outside!
transformToResult(SoftPathModel.SoftMatrixEntry[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
This method should not be called from outside!
transformToResult(SoftAlignmentScoreAlgorithm.ScoreEntry[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
This method should not be called from outside!
transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence, double[][]>, double[][], double[], double[], double[], double[], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentFullAlgorithm
This method should not be called from outside!
transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence, double[][]>, double[][], double[], double[], double[], double[], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.SoftLocalAlignmentScoreAlgorithm
This method should not be called from outside!
transformToResult(StrictAlignmentFullAlgorithm.FullMatrixEntry[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm
This method should not be called from outside!
transformToResult(StrictAlignmentScoreAlgorithm.ScoreEntry[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
This method should not be called from outside!
transformToResult(StrictAllOptimalAlgorithm.FullMatrixEntry[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
This method should not be called from outside!
transformToResult(double[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.StrictDTWFullAlgorithm
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[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.StrictDTWScoreAlgorithm
This method has to be implemented by sub classes to transform a calculated dynamic programming matrix to a valid result of that implementation.
transformToResult(StrictAllOptimalAlgorithm.FullMatrixEntry[][], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
This method should not be called from outside!
transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence, double[][]>, double[][], double[], double[], double[], double[], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.StrictLocalAlignmentFullAlgorithm
This method should not be called from outside!
transformToResult(EnumMap<AbstractLocalAlignmentAlgorithm.Recurrence, double[][]>, double[][], double[], double[], double[], double[], Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.StrictLocalAlignmentScoreAlgorithm
This method should not be called from outside!
TrivialEditComparator - Class in de.unibi.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.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
 
TYPE_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
 

U

Utils - Class in de.unibi.citec.tcs.alignment.visualization
 
Utils() - Constructor for class de.unibi.citec.tcs.alignment.visualization.Utils
 

V

validate(Value) - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
 
validate(Value) - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
validate(Value) - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialKeywordSpecification
Value - Interface in de.unibi.citec.tcs.alignment.sequence
This represents a single value for a keyword in a given node.
valueOf(String) - Static method in enum de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm.Recurrence
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unibi.citec.tcs.alignment.comparators.NCDComparator.CompressorType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unibi.citec.tcs.alignment.OperationType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unibi.citec.tcs.alignment.ScoreBasedWeighting
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unibi.citec.tcs.alignment.sequence.ValueType
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.unibi.citec.tcs.alignment.AbstractLocalAlignmentAlgorithm.Recurrence
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unibi.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.unibi.citec.tcs.alignment.OperationType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unibi.citec.tcs.alignment.ScoreBasedWeighting
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unibi.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.unibi.citec.tcs.alignment.sequence
This defines all possible types of values.
VectorialKeywordSpecification - Class in de.unibi.citec.tcs.alignment.sequence
This specifies vectors by their length.
VectorialKeywordSpecification(int, String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.VectorialKeywordSpecification
 
VectorialSequences - Class in de.unibi.citec.tcs.alignment.wrappers
This provides an easier interface for simple vectorial sequences.
VectorialSequences() - Constructor for class de.unibi.citec.tcs.alignment.wrappers.VectorialSequences
 
VectorialValue - Class in de.unibi.citec.tcs.alignment.sequence
This value is reserved for numeric vectors, represented internally as doubles.
VectorialValue() - Constructor for class de.unibi.citec.tcs.alignment.sequence.VectorialValue
 
VectorialValue(double[]) - Constructor for class de.unibi.citec.tcs.alignment.sequence.VectorialValue
 
VectorialValue(Object) - Constructor for class de.unibi.citec.tcs.alignment.sequence.VectorialValue
 
Visualization - Class in de.unibi.citec.tcs.alignment.visualization
Visualizes given alignments in clear and adaptable tables.
Visualization() - Constructor for class de.unibi.citec.tcs.alignment.visualization.Visualization
 

W

writeFile(String, String) - Static method in class de.unibi.citec.tcs.alignment.visualization.Utils
Writes the given text to a file.
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Copyright (C) 2013, 2014 Benjamin Paaßen, Charlie Krüger, Georg Zentgraf, AG Theoretical Computer Science, Centre of Excellence Cognitive Interaction Technology (CITEC), University of Bielefeld, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/tcs