- 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.
- 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!
- 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.
- 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
-
- 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
-