- calc_weighted_comp_sum(Comparator[], double[], int[], Node, Node) - Static method in class de.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.citec.tcs.alignment.parallel.Engine
-
Starts the actual, parallel computation.
- calculateAlignment(Sequence, Sequence) - Method in class de.citec.tcs.alignment.AbstractAffineAlignmentAlgorithm
-
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.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.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 class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
-
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.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.citec.tcs.alignment.KernelDTWFullAlgorithm
-
This calculates the alignment between the Sequences a and b and returns
it as an instance of the result class for this algorithm.
- calculateComparatorDistances(OperationType, Node, Node, AlignmentSpecification) - Static method in class de.citec.tcs.alignment.Operation
-
- calculateCompressedSize(String) - Method in enum de.citec.tcs.alignment.comparators.NCDComparator.CompressorType
-
Calculates the compressed size of the given input string in bytes.
- calculateDeletionCosts(Node) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
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.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.citec.tcs.alignment.wrappers.StringEditDistance
-
Calculates the pairwise alignment derivative between all given input
sequences using the given algorithm.
- calculateInsertionCosts(Node) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
This calculates the non-weighted costs for inserting the single values of
node b.
- calculateLocalDerivative(int, V, V, OperationType) - Method in class de.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.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.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.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.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.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 class de.citec.tcs.alignment.adp.SoftADPPathModel
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateParameterDerivative(DerivableComparator<X, Y>, String) - Method in interface de.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.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.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.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.citec.tcs.alignment.SoftAffinePathModel
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.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.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 class de.citec.tcs.alignment.adp.SoftADPPathModel
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateRawParameterDerivative(DerivableComparator<X, Y>, String) - Method in interface de.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.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.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.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.citec.tcs.alignment.SoftAffinePathModel
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateRawParameterDerivative(DerivableComparator<X, Y>, String) - Method in class de.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.citec.tcs.alignment.SoftPathModel
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateReplacementCosts(Node, Node) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
This calculates the non-weighted costs for replacing the single values in
node a by the values in node b.
- calculateSkipDeletionCosts(Node) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
This calculates the non-weighted costs for skip-deleting the single
values in node a.
- calculateSkipInsertionCosts(Node) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
This calculates the non-weighted costs for skip-inserting the single
values of node b.
- calculateSoftminDerivatives(double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
-
Calculates the softmin'(x_i) function for all variables x_i in the
given input.
- calculateSoftminDerivatives(double, double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
-
Calculates the softmin'(x_i) function for all variables x_i in the
given input.
- calculateSoftminProbabilities(double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
-
Calculates the softmin probabilities p_i for the given beta and
the given variables.
- calculateSoftminProbabilities(double, double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
-
Calculates the softmin probabilities p_i for the given beta and
the given variables.
- calculateSparseLocalDerivative(V, V, OperationType) - Method in class de.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.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.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.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 class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in interface de.citec.tcs.alignment.AlignmentDerivativeAlgorithm
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.citec.tcs.alignment.AlignmentPath
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.citec.tcs.alignment.PathList
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.citec.tcs.alignment.PathMap
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.citec.tcs.alignment.SoftDTWModel
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.citec.tcs.alignment.SoftPathModel
-
Calculates the derivative for each keyword weight.
- calculateWeighting(Collection<Double>) - Method in enum de.citec.tcs.alignment.ScoreBasedWeighting
-
- calculateWeighting(double[]) - Method in enum de.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.citec.tcs.alignment.comparators
-
This compares strings using statistics over the number of letters inside.
- CharStatComparator() - Constructor for class de.citec.tcs.alignment.comparators.CharStatComparator
-
- choice(double...) - Method in class de.citec.tcs.alignment.AbstractAffineAlignmentAlgorithm
-
This should implement the choice function as the term is used
in the Bellman's Gap context.
- choice(double[]) - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
-
This should implement the choice function as the term is used
in the Bellman's Gap context.
- choice(double[]) - Method in class de.citec.tcs.alignment.adp.SoftADPFullAlgorithm
-
This should implement the choice function as the term is used
in the Bellman's Gap context.
- choice(double[]) - Method in class de.citec.tcs.alignment.adp.SoftADPScoreAlgorithm
-
This should implement the choice function as the term is used
in the Bellman's Gap context.
- choice(double[]) - Method in class de.citec.tcs.alignment.adp.StrictADPFullAlgorithm
-
This should implement the choice function as the term is used
in the Bellman's Gap context.
- choice(double[]) - Method in class de.citec.tcs.alignment.adp.StrictADPScoreAlgorithm
-
This should implement the choice function as the term is used
in the Bellman's Gap context.
- choice(double...) - Method in class de.citec.tcs.alignment.SoftAffineAlignmentFullAlgorithm
-
This implements the strict maximum of the given input doubles.
- choice(double...) - Method in class de.citec.tcs.alignment.SoftAffineAlignmentScoreAlgorithm
-
This implements the strict maximum of the given input doubles.
- choice(double...) - Method in class de.citec.tcs.alignment.StrictAffineAlignmentFullAlgorithm
-
This implements the strict maximum of the given input doubles.
- choice(double...) - Method in class de.citec.tcs.alignment.StrictAffineAlignmentScoreAlgorithm
-
This implements the strict maximum of the given input doubles.
- clearTasks() - Method in class de.citec.tcs.alignment.parallel.Engine
-
Removes all tasks from this Engine.
- clone() - Method in class de.citec.tcs.alignment.AlignmentPath
- clone() - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
- CommandLineProgressReporter - Class in de.citec.tcs.alignment.parallel
-
This is a default ProgressReporter that writes a notification to the command
line after progressReportStepSize percent of computation are finished.
- CommandLineProgressReporter() - Constructor for class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
-
- Comparator<X extends Value> - Interface in de.citec.tcs.alignment.comparators
-
This defines a function that returns a (normalized) dissimilarity between
values of a certain value space.
- compare(StringValue, StringValue) - Method in class de.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.
1 means maximum dissimilarity between a and b.
0 means maximum similarity between a and b (especially it should be
true that a = b implies a zero distance).
distance(a,b) should be equal or at least close to
distance(b,a)
Please note that this has to be well-defined, even if an input is null.
- compare(X, X) - Method in interface de.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.
1 means maximum dissimilarity between a and b.
0 means maximum similarity between a and b (especially it should be
true that a = b implies a zero distance).
distance(a,b) should be equal or at least close to
distance(b,a)
Please note that this has to be well-defined, even if an input is null.
- compare(VectorialValue, VectorialValue) - Method in class de.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.
1 means maximum dissimilarity between a and b.
0 means maximum similarity between a and b (especially it should be
true that a = b implies a zero distance).
distance(a,b) should be equal or at least close to
distance(b,a)
Please note that this has to be well-defined, even if an input is null.
- compare(VectorialValue, VectorialValue) - Method in class de.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.
1 means maximum dissimilarity between a and b.
0 means maximum similarity between a and b (especially it should be
true that a = b implies a zero distance).
distance(a,b) should be equal or at least close to
distance(b,a)
Please note that this has to be well-defined, even if an input is null.
- compare(VectorialValue, VectorialValue) - Method in class de.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.
1 means maximum dissimilarity between a and b.
0 means maximum similarity between a and b (especially it should be
true that a = b implies a zero distance).
distance(a,b) should be equal or at least close to
distance(b,a)
Please note that this has to be well-defined, even if an input is null.
- compare(StringValue, StringValue) - Method in class de.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.
1 means maximum dissimilarity between a and b.
0 means maximum similarity between a and b (especially it should be
true that a = b implies a zero distance).
distance(a,b) should be equal or at least close to
distance(b,a)
Please note that this has to be well-defined, even if an input is null.
- compare(SymbolicValue, SymbolicValue) - Method in class de.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.
1 means maximum dissimilarity between a and b.
0 means maximum similarity between a and b (especially it should be
true that a = b implies a zero distance).
distance(a,b) should be equal or at least close to
distance(b,a)
Please note that this has to be well-defined, even if an input is null.
- compare(SymbolicValue, SymbolicValue) - Method in class de.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.
1 means maximum dissimilarity between a and b.
0 means maximum similarity between a and b (especially it should be
true that a = b implies a zero distance).
distance(a,b) should be equal or at least close to
distance(b,a)
Please note that this has to be well-defined, even if an input is null.
- compare(VectorialValue, VectorialValue) - Method in class de.citec.tcs.alignment.comparators.ZeroNormComparator
-
This has to return a distance between a and b with the following
restrictions:
The return value has to lie between 0 and 1.
1 means maximum dissimilarity between a and b.
0 means maximum similarity between a and b (especially it should be
true that a = b implies a zero distance).
distance(a,b) should be equal or at least close to
distance(b,a)
Please note that this has to be well-defined, even if an input is null.
- compareTo(DPCellId) - Method in class de.citec.tcs.alignment.adp.DPCellId
-
- compareTo(MatrixEngine.MatrixCoordinate) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine.MatrixCoordinate
- ComparisonBasedSkipExtendedComparator<V extends Value> - Class in de.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.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
- comparisonDerivative(int, StringValue, StringValue) - Method in class de.citec.tcs.alignment.comparators.CharStatComparator
-
This should implement the local derivative calculation in case of
comparisons.
- comparisonDerivative(int, VectorialValue, VectorialValue) - Method in class de.citec.tcs.alignment.comparators.EuclideanComparator
-
This should implement the local derivative calculation in case of
comparisons.
- comparisonDerivative(int, VectorialValue, VectorialValue) - Method in class de.citec.tcs.alignment.comparators.L1NormComparator
-
This should implement the local derivative calculation in case of
comparisons.
- comparisonDerivative(int, StringValue, StringValue) - Method in class de.citec.tcs.alignment.comparators.NCDComparator
-
This should implement the local derivative calculation in case of
comparisons.
- comparisonDerivative(int, V, V) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
This should implement the local derivative calculation in case of
comparisons.
- comparisonDerivative(int, SymbolicValue, SymbolicValue) - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
-
This should implement the local derivative calculation in case of
comparisons.
- comparisonDerivative(int, VectorialValue, VectorialValue) - Method in class de.citec.tcs.alignment.comparators.ZeroNormComparator
-
This should implement the local derivative calculation in case of
comparisons.
- containsGaps() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType DELETION
or INSERTION.
- containsGaps() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType DELETION
or INSERTION.
- containsGaps() - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType DELETION
or INSERTION.
- containsGaps() - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType DELETION
or INSERTION.
- containsGaps() - Method in interface de.citec.tcs.alignment.adp.Grammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType DELETION
or INSERTION.
- containsSkips() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType SKIPDELETION
or SKIPINSERTION.
- containsSkips() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType SKIPDELETION
or SKIPINSERTION.
- containsSkips() - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType SKIPDELETION
or SKIPINSERTION.
- containsSkips() - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType SKIPDELETION
or SKIPINSERTION.
- containsSkips() - Method in interface de.citec.tcs.alignment.adp.Grammar
-
This should return true if and only if this grammar contains
at least one production rule with the OperationType SKIPDELETION
or SKIPINSERTION.
- createCallable(MatrixEngine.MatrixCoordinate) - Method in class de.citec.tcs.alignment.AbstractParallelDerivativeEngine
-
A method that should create a Callable (computation job) for the given
identifier object.
- createCallable(I) - Method in class de.citec.tcs.alignment.parallel.Engine
-
A method that should create a Callable (computation job) for the given
identifier object.
- createCallable(MatrixEngine.MatrixCoordinate) - Method in class de.citec.tcs.alignment.ParallelProcessingEngine
-
A method that should create a Callable (computation job) for the given
identifier object.
- createCallableWithAlgorithm(AlignmentDerivativeAlgorithm) - Method in class de.citec.tcs.alignment.AbstractParallelDerivativeEngine
-
Instead of a matrix coordinate identifier, this method should create a
fitting calculation job for the derivative with the given
AlignmentDerivativeAlgorithm.
- createCallableWithAlgorithm(AlignmentDerivativeAlgorithm) - Method in class de.citec.tcs.alignment.ParallelDerivativeEngine
-
Instead of a matrix coordinate identifier, this method should create a
fitting calculation job for the derivative with the given
AlignmentDerivativeAlgorithm.
- createCallableWithAlgorithm(AlignmentDerivativeAlgorithm) - Method in class de.citec.tcs.alignment.ParallelRawDerivativeEngine
-
Instead of a matrix coordinate identifier, this method should create a
fitting calculation job for the derivative with the given
AlignmentDerivativeAlgorithm.
- createCallableWithAlgorithm(AlignmentDerivativeAlgorithm) - Method in class de.citec.tcs.alignment.ParallelWeightDerivativeEngine
-
Instead of a matrix coordinate identifier, this method should create a
fitting calculation job for the derivative with the given
AlignmentDerivativeAlgorithm.
- createDelInitial(X, int, double) - Method in class de.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
- createDelInitial(SoftPathModel.SoftMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
- createDelInitial(SoftPathModel.SoftMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
- createDelInitial(SoftAlignmentScoreAlgorithm.ScoreEntry, int, double) - Method in class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
- createDelInitial(StrictAlignmentFullAlgorithm.FullMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
- createDelInitial(StrictAlignmentScoreAlgorithm.ScoreEntry, int, double) - Method in class de.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
- createDelInitial(StrictAllOptimalAlgorithm.FullMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
- createDelInitial(StrictAllOptimalAlgorithm.FullMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.StrictKPathAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,0) of the alignment matrix with
this method given the entry (i,0).
- createGenericArray(int, Class<X>) - Static method in class de.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.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.citec.tcs.alignment.parallel.MatrixEngine
-
This is a helper method that creates an object matrix of the given class.
- createInitial() - Method in class de.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
- createInitial() - Method in class de.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
- createInitial() - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
- createInitial() - Method in class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
- createInitial() - Method in class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
- createInitial() - Method in class de.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
- createInitial() - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
- createInitial() - Method in class de.citec.tcs.alignment.StrictKPathAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
- createInsInitial(X, int, double) - Method in class de.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
- createInsInitial(SoftPathModel.SoftMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
- createInsInitial(SoftPathModel.SoftMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
- createInsInitial(SoftAlignmentScoreAlgorithm.ScoreEntry, int, double) - Method in class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
- createInsInitial(StrictAlignmentFullAlgorithm.FullMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
- createInsInitial(StrictAlignmentScoreAlgorithm.ScoreEntry, int, double) - Method in class de.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
- createInsInitial(StrictAllOptimalAlgorithm.FullMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
- createInsInitial(StrictAllOptimalAlgorithm.FullMatrixEntry, int, double) - Method in class de.citec.tcs.alignment.StrictKPathAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,j+1) of the alignment matrix with
this method given the entry (0,j).
- createNewEntry(X, X, X, int, int, double, double, double) - Method in class de.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
- createNewEntry(SoftPathModel.SoftMatrixEntry, SoftPathModel.SoftMatrixEntry, SoftPathModel.SoftMatrixEntry, int, int, double, double, double) - Method in class de.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
- createNewEntry(SoftPathModel.SoftMatrixEntry, SoftPathModel.SoftMatrixEntry, SoftPathModel.SoftMatrixEntry, int, int, double, double, double) - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
- createNewEntry(SoftAlignmentScoreAlgorithm.ScoreEntry, SoftAlignmentScoreAlgorithm.ScoreEntry, SoftAlignmentScoreAlgorithm.ScoreEntry, int, int, double, double, double) - Method in class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
- createNewEntry(StrictAlignmentFullAlgorithm.FullMatrixEntry, StrictAlignmentFullAlgorithm.FullMatrixEntry, StrictAlignmentFullAlgorithm.FullMatrixEntry, int, int, double, double, double) - Method in class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
- createNewEntry(StrictAlignmentScoreAlgorithm.ScoreEntry, StrictAlignmentScoreAlgorithm.ScoreEntry, StrictAlignmentScoreAlgorithm.ScoreEntry, int, int, double, double, double) - Method in class de.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
- createNewEntry(StrictAllOptimalAlgorithm.FullMatrixEntry, StrictAllOptimalAlgorithm.FullMatrixEntry, StrictAllOptimalAlgorithm.FullMatrixEntry, int, int, double, double, double) - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
- createNewEntry(StrictAllOptimalAlgorithm.FullMatrixEntry, StrictAllOptimalAlgorithm.FullMatrixEntry, StrictAllOptimalAlgorithm.FullMatrixEntry, int, int, double, double, double) - Method in class de.citec.tcs.alignment.StrictKPathAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (i+1,j+1) of the alignment matrix with
this method given the entries (i,j+1) (deletion), (i+1,j) (insertion) and
(i,j) (replacement).
- GapAlignmentAlgorithm<R> - Interface in de.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.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.citec.tcs.alignment.comparators.ReplacementCosts
-
- generateSequences(int, int, int) - Static method in class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
-
This generates N random sequences of length L each with K keywords.
- generateSequences(int, int, NodeSpecification) - Static method in class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
-
This generates N random sequences of length L each according to
the given NodeSpecification.
- generateSpecification(int) - Static method in class de.citec.tcs.alignment.wrappers.RandomSequenceGenerator
-
This generates an AlignmentSpecification and implicitly a
NodeSpecification for K keywords.
- get(int, int) - Method in class de.citec.tcs.alignment.SparseMatrix
-
Returns the value stored at the given position or null if no value was
stored there until now.
- getAccepting() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
-
Returns the set of all accepting nonterminals of this grammar.
- getAccepting() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
-
Returns the set of all accepting nonterminals of this grammar.
- getAccepting() - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
-
Returns the set of all accepting nonterminals of this grammar.
- getAccepting() - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
-
Returns the set of all accepting nonterminals of this grammar.
- getAccepting() - Method in interface de.citec.tcs.alignment.adp.Grammar
-
Returns the set of all accepting nonterminals of this grammar.
- getAdditionalColumns() - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
-
Optionally you may manipulate this list to add or remove additional
columns for the HTML table.
- getAlgorithm() - Method in class de.citec.tcs.alignment.ParallelProcessingEngine
-
- getAllPaths() - Method in class de.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.citec.tcs.alignment.comparators.HyperbolicNormalizer
-
- getAlphabet() - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- getAlphabet() - Method in class de.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
-
Returns the Alphabet that defines which symbols are allowed for this
keyword.
- getAlphabet() - Method in class de.citec.tcs.alignment.sequence.SymbolicValue
-
Returns the Alphabet that defines which symbols are allowed for this
keyword.
- getApproxThreshold() - Method in class de.citec.tcs.alignment.adp.SoftADPFullAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- getApproxThreshold() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- getApproxThreshold() - Method in class de.citec.tcs.alignment.adp.SoftADPScoreAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- getApproxThreshold() - Method in class de.citec.tcs.alignment.SoftAffineAlignmentFullAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- getApproxThreshold() - Method in class de.citec.tcs.alignment.SoftAffineAlignmentScoreAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- getApproxThreshold() - Method in class de.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
Returns the threshold for which exponents within the softmin function
will be disregarded.
- getApproxThreshold() - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
Returns the threshold for which exponents within the softmin function
will be disregarded.
- getApproxThreshold() - Method in class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- getAxiom() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
-
Returns the axiom of this grammar.
- getAxiom() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
-
Returns the axiom of this grammar.
- getAxiom() - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
-
Returns the axiom of this grammar.
- getAxiom() - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
-
Returns the axiom of this grammar.
- getAxiom() - Method in interface de.citec.tcs.alignment.adp.Grammar
-
Returns the axiom of this grammar.
- getBeta() - Method in class de.citec.tcs.alignment.adp.SoftADPFullAlgorithm
-
- getBeta() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the parameter defining the "softness" of the alignment.
- getBeta() - Method in class de.citec.tcs.alignment.adp.SoftADPScoreAlgorithm
-
Returns the parameter defining the "softness" of the alignment.
- getBeta() - Method in class de.citec.tcs.alignment.comparators.ExponentialNormalizer
-
- getBeta() - Method in class de.citec.tcs.alignment.SoftAffineAlignmentFullAlgorithm
-
Returns the parameter defining the "softness" of the alignment.
- getBeta() - Method in class de.citec.tcs.alignment.SoftAffineAlignmentScoreAlgorithm
-
Returns the parameter defining the "softness" of the alignment.
- getBeta() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the parameter defining the "softness" of the alignment.
- getBeta() - Method in class de.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
- getBeta() - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
- getBeta() - Method in class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
- getBeta() - Method in class de.citec.tcs.alignment.SoftPathModel
-
The parameter defining the "softness" of the alignment.
- getComparator(String) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
Returns the Comparator that is currently set for the given keyword.
- getComparator(int) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
Returns the Comparator that is currently set for the given keyword.
- getComparatorDistances() - Method in class de.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.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the matrix of comparison costs between both input sequences.
- getCompareMatrix() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the matrix of comparison costs between both input sequences.
- getCompressor() - Method in class de.citec.tcs.alignment.comparators.NCDComparator
-
- getCostMatrix() - Method in class de.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.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns the cost matrix itself.
- getCSS() - Method in class de.citec.tcs.alignment.visualization.AbstractHTMLColumn
-
This default implementation returns an empty string.
- getCSS() - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
-
This method should return CSS code containing styling rules for this
column.
- getCSS() - Method in class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
This default implementation returns an empty string.
- getDecimalPlaces() - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
-
This specifies how many decimal places (after comma) should be
visualized.
- getDefaultComparator(KeywordSpecification) - Static method in class de.citec.tcs.alignment.comparators.Defaults
-
Returns a sensible default comparator for the given KeywordSpecification.
- getDefaultComparators(KeywordSpecification[]) - Static method in class de.citec.tcs.alignment.comparators.Defaults
-
Returns sensible default comparators for the given KeywordSpecifications.
- getDefaultComparators(NodeSpecification) - Static method in class de.citec.tcs.alignment.comparators.Defaults
-
Returns sensible default comparators for the given NodeSpecification, one
for each contained KeywordSpecification.
- getDelCosts() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getDeleteComparison() - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Returns the comparison value that is used to compute the cost of
deletions if the dynamic flag is set to true.
- getDeletionCost(String) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- getDeletionCost() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
Returns the (constant) cost for deleting a value.
- getDeletionCosts() - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns all deletion costs without any other costs.
- getDeletionMatrix() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the vector of deletion costs.
- getDeletionMatrix() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the vector of deletion costs.
- getDelLocal() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getDelLocal() - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getDelProb() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getDelSoftDerivative() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getDerivative() - Method in class de.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- getDifference(AlignmentPath) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
-
Returns the difference at each operation of the given AlignmentPath.
- getDistance() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the distance between the two input sequences of this Derivative.
- getDistance() - Method in interface de.citec.tcs.alignment.AlignmentDerivativeAlgorithm
-
Returns the distance between the two input sequences of this Derivative.
- getDistance() - Method in class de.citec.tcs.alignment.AlignmentPath
-
Returns the distance between the two input sequences of this Derivative.
- getDistance() - Method in class de.citec.tcs.alignment.PathList
-
Returns the average distance of all stored paths.
- getDistance() - Method in class de.citec.tcs.alignment.PathMap
-
Returns the average distance of all stored paths.
- getDistance() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the distance between the two input sequences of this Derivative.
- getDistance() - Method in class de.citec.tcs.alignment.SoftDTWModel
-
Returns the distance between the two input sequences of this Derivative.
- getDistance() - Method in class de.citec.tcs.alignment.SoftPathModel
-
Returns the distance between the two input sequences of this Derivative.
- getDoubleResultMatrix() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Returns the results of the calculation as a primitive double matrix.
- getDp_tables() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the dynamic programming tables that constitute the (soft) affine
alignment of both input sequences.
- getDpTables() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the dynamic programming tables that constitute the soft
alignment of both input sequences.
- getEntryClass() - Method in class de.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
Returns the class of matrix entries.
- getExtensions(AlignmentPath) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
-
Returns the sequence extensions modelled by this AlignmentPath.
- getGenericClass(Grammar<N>) - Static method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the generic class of a SoftADPPathModel given a grammar.
- getGrammar() - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
-
Returns the ADP grammar that is used as basis of this ADPAlgorithm.
- getGrammar() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the ADP grammar that was used to compute this SoftADPPathModel.
- getHTML(Operation) - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
-
This method should return one or multiple td-tags (corresponding to
the return value of getNumColumns()) containing the additional
information for the given alignment Operation.
- getHTML(Operation) - Method in class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
This method should return one or multiple td-tags (corresponding to
the return value of getNumColumns()) containing the additional
information for the given alignment Operation.
- getHTML(Operation) - Method in class de.citec.tcs.alignment.visualization.ValueColumn
-
This method should return one or multiple td-tags (corresponding to
the return value of getNumColumns()) containing the additional
information for the given alignment Operation.
- getI() - Method in class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- getI() - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getIdentClass() - Method in class de.citec.tcs.alignment.parallel.Engine
-
Returns the class of objects to identify jobs for this Engine.
- getInsCosts() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getInsertComparison() - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Returns the comparison value that is used to compute the cost of
insertions if the dynamic flag is set to true.
- getInsertionCost(String) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- getInsertionCost() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
Returns the (constant) cost for inserting a value.
- getInsertionCosts() - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns all insertion costs without any other costs.
- getInsertionMatrix() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the vector of insertion costs.
- getInsertionMatrix() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the vector of insertion costs.
- getInsLocal() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getInsLocal() - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getInsProb() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getInsSoftDerivative() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getJ() - Method in class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- getJ() - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getJS() - Method in class de.citec.tcs.alignment.visualization.AbstractHTMLColumn
-
This default implementation returns an empty string.
- getJS() - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
-
This method should return JavaScript containing code relevant
for this column.
- getKey() - Method in class de.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- getKeyword(int) - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
-
Returns the keyword for the given index.
- getKeyword() - Method in class de.citec.tcs.alignment.sequence.KeywordSpecification
-
Returns the keyword.
- getKeyword() - Method in class de.citec.tcs.alignment.visualization.AbstractHTMLColumn
-
This method should return the keyword of this column.
- getKeyword() - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
-
This method should return the keyword of this column.
- getKeywordIndex(String) - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
-
Returns the index of the given keyword.
- getKeywords() - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
-
Returns the keywords that are mapped.
- getKeywords() - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
-
Optionally you may manipulate this set to restrict the keywords for which
the HTMLVisualizer will print columns in the html table.
- getKeywordSpecification(String) - Method in class de.citec.tcs.alignment.sequence.NodeSpecification
-
Returns the specification for the given keyword.
- getKeywordSpecification(int) - Method in class de.citec.tcs.alignment.sequence.NodeSpecification
-
Returns the specification for the given keyword.
- getKeywordSpecifications() - Method in class de.citec.tcs.alignment.sequence.NodeSpecification
-
- getLastAlignmentMatrix() - Method in class de.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
The last matrix that was calculated using this algorithm.
- getLastDTWMatrix() - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
-
This returns the dynamic programming matrix that was calculated
in the last call of calculateAlignment.
- getLeft() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the left sequence of this derivative.
- getLeft() - Method in interface de.citec.tcs.alignment.AlignmentDerivativeAlgorithm
-
Returns the left sequence of this derivative.
- getLeft() - Method in class de.citec.tcs.alignment.AlignmentPath
-
Returns the left sequence of this derivative.
- getLeft() - Method in class de.citec.tcs.alignment.Operation
-
- getLeft() - Method in class de.citec.tcs.alignment.PathList
-
Returns the left sequence of this derivative.
- getLeft() - Method in class de.citec.tcs.alignment.PathMap
-
Returns the left sequence of this derivative.
- getLeft() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the left sequence of this derivative.
- getLeft() - Method in class de.citec.tcs.alignment.SoftDTWModel
-
Returns the left sequence of this derivative.
- getLeft() - Method in class de.citec.tcs.alignment.SoftPathModel
-
Returns the left sequence of this derivative.
- getLength() - Method in class de.citec.tcs.alignment.sequence.VectorialKeywordSpecification
-
The length all vectors for this keyword have to have.
- getM() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Returns the number of rows in the matrix.
- getMatchCost() - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
-
Returns the cost for matches (0 per default).
- getMax() - Method in class de.citec.tcs.alignment.comparators.AffineNormalizer
-
Returns the maximum possible value, which will be mapped to 1.
- getMin() - Method in class de.citec.tcs.alignment.comparators.AffineNormalizer
-
Returns the minimum possible value, which will be mapped to 0.
- getMinMiddleSkips() - Method in class de.citec.tcs.alignment.AbstractAffineAlignmentAlgorithm
-
The minimum number of skips that have to be done in the middle
of an alignment.
- getMinMiddleSkips() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
-
Returns the minimum number of skip operations that are required
for a skip-region in the middle to be permitted.
- getMinMiddleSkips() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
The minimum number of skips that have to be done in the middle
of an alignment.
- getMismatchCost() - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
-
Returns the cost for mismatches (1 per default).
- getN() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Returns the number of columns in the matrix.
- getNodes() - Method in class de.citec.tcs.alignment.sequence.Sequence
-
Returns the actual list of nodes.
- getNodeSpecification() - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
- getNodeSpecification() - Method in class de.citec.tcs.alignment.sequence.Sequence
-
Returns the NodeSpecification all Nodes in this sequence belong to.
- getNonterminal() - Method in class de.citec.tcs.alignment.adp.ProductionRule
-
Returns the target nonterminal symbol of this rule.
- getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.AffineGrammar
-
Returns the enum class that lists the nonterminal symbols of
this grammar.
- getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
-
Returns the enum class that lists the nonterminal symbols of
this grammar.
- getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
-
Returns the enum class that lists the nonterminal symbols of
this grammar.
- getNonterminalClass() - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
-
Returns the enum class that lists the nonterminal symbols of
this grammar.
- getNonterminalClass() - Method in interface de.citec.tcs.alignment.adp.Grammar
-
Returns the enum class that lists the nonterminal symbols of
this grammar.
- getNormalizer() - Method in class de.citec.tcs.alignment.comparators.EuclideanComparator
-
Please refer to the corresponding setter method for more information.
- getNormalizer() - Method in class de.citec.tcs.alignment.comparators.L1NormComparator
-
Please refer to the corresponding setter method for more information.
- getNumberOfComparisonParameters() - Method in class de.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.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.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.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.citec.tcs.alignment.comparators.SkipExtendedComparator
-
Implementing classes should return the number of (derivative-relevant)
parameters used for the compare-function.
- getNumberOfComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
-
Implementing classes should return the number of (derivative-relevant)
parameters used for the compare-function.
- getNumberOfComparisonParameters() - Method in class de.citec.tcs.alignment.comparators.ZeroNormComparator
-
Implementing classes should return the number of (derivative-relevant)
parameters used for the compare-function.
- getNumberOfParameters() - Method in interface de.citec.tcs.alignment.comparators.DerivableComparator
-
This shall return the number of parameters of this comparator.
- getNumberOfParameters() - Method in class de.citec.tcs.alignment.comparators.DTWKernelComparator
-
- getNumberOfParameters() - Method in class de.citec.tcs.alignment.comparators.ReplacementComparator
-
This shall return the number of parameters of this comparator.
- getNumberOfParameters() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
This shall return the number of parameters of this comparator.
- getNumberOfThreads() - Method in class de.citec.tcs.alignment.parallel.Engine
-
Returns the number of threads that are used for computation (16 per
default).
- getNumColumns() - Method in interface de.citec.tcs.alignment.visualization.HTMLColumn
-
This method should return the number of HTML columns occupied by
this column.
- getNumColumns() - Method in class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
This method should return the number of HTML columns occupied by
this column.
- getNumColumns() - Method in class de.citec.tcs.alignment.visualization.ValueColumn
-
This method should return the number of HTML columns occupied by
this column.
- getOperations() - Method in class de.citec.tcs.alignment.adp.ProductionRule
-
Returns the operations that are applied in this production rule.
- getOperations() - Method in class de.citec.tcs.alignment.AlignmentPath
-
- getOriginalIndex(int) - Method in class de.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.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- getPath() - Method in class de.citec.tcs.alignment.Operation
-
- getPathLimit() - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
Returns the the number of paths that shall be sampled.
- getPathLimit() - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm
-
Please refer to the corresponding setter-method for more information.
- getPathLimit() - Method in class de.citec.tcs.alignment.StrictKPathAlgorithm
-
Please refer to the corresponding setter method for more calculation.
- getPathMatrix() - Method in class de.citec.tcs.alignment.SoftPathModel
-
This is the dynamic programming matrix calculated by a
SoftAlignmentAlgorithm.
- getPaths(double) - Method in class de.citec.tcs.alignment.PathMap
-
Returns all paths with the given score.
- getPossibleRules(AffineGrammar.Nonterminal, int, int) - Method in class de.citec.tcs.alignment.adp.AffineGrammar
-
Returns all production rules of this grammar that can be applied
in the current situation.
- getPossibleRules(N, int, int) - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
-
Returns all production rules of this grammar that can be applied
in the current situation.
- getPossibleRules(GlobalAsymmetricGrammar.Nonterminal, int, int) - Method in class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
-
Returns all production rules of this grammar that can be applied
in the current situation.
- getPossibleRules(GlobalGrammar.Nonterminal, int, int) - Method in class de.citec.tcs.alignment.adp.GlobalGrammar
-
Returns all production rules of this grammar that can be applied
in the current situation.
- getPossibleRules(N, int, int) - Method in interface de.citec.tcs.alignment.adp.Grammar
-
Returns all production rules of this grammar that can be applied
in the current situation.
- getPredecessor() - Method in class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- getPreferredCooptimal() - Method in class de.citec.tcs.alignment.StrictAffineAlignmentFullAlgorithm
-
This allows to specify an order in which operations shall be preferred if
cooptimal alignments occur.
- getProgressReportStepSize() - Method in class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
-
Returns the percent of computation that have to be completed until a new
notification is written to the command line.
- getProperty(String) - Static method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
-
- getRepCosts() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getReplacementCost(String, String) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- getReplacementCosts() - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns the whole matrix of replacement costs without gap and skip costs.
- getRepLocal() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getRepLocal() - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getReporter() - Method in class de.citec.tcs.alignment.parallel.Engine
-
Returns the ProgressReporter that is used to report progress.
- getRepProb() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getRepSoftDerivative() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getResultClass() - Method in class de.citec.tcs.alignment.AbstractAffineAlignmentAlgorithm
-
This method shall return the class of the alignment result.
- getResultClass() - Method in class de.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This method shall return the class of the alignment result.
- getResultClass() - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
-
This method shall return the class of the alignment result.
- getResultClass() - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
-
This method shall return the class of the alignment result.
- getResultClass() - Method in interface de.citec.tcs.alignment.AlignmentAlgorithm
-
This method shall return the class of the alignment result.
- getResultClass() - Method in interface de.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.citec.tcs.alignment.comparators.DTWKernelComparator
-
- getResultClass() - Method in class de.citec.tcs.alignment.comparators.ReplacementComparator
-
Returns the class of the intuitive format of the derivatives for all
parameters of this comparator.
- getResultClass() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
- getResultClass() - Method in class de.citec.tcs.alignment.KernelDTWFullAlgorithm
-
This method shall return the class of the alignment result.
- getResultClass() - Method in class de.citec.tcs.alignment.parallel.Engine
-
Returns the class of result objects of jobs in this Engine.
- getResultMatrix() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Returns the results of the calculation as an object matrix.
- getResults() - Method in class de.citec.tcs.alignment.parallel.Engine
-
Returns the results of this Engines last computation.
- getRGBColor(double) - Static method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
-
Returns an hexadecimal rgb color string for the given score.
- getRight() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the right sequence of this derivative.
- getRight() - Method in interface de.citec.tcs.alignment.AlignmentDerivativeAlgorithm
-
Returns the right sequence of this derivative.
- getRight() - Method in class de.citec.tcs.alignment.AlignmentPath
-
Returns the right sequence of this derivative.
- getRight() - Method in class de.citec.tcs.alignment.Operation
-
- getRight() - Method in class de.citec.tcs.alignment.PathList
-
Returns the right sequence of this derivative.
- getRight() - Method in class de.citec.tcs.alignment.PathMap
-
Returns the right sequence of this derivative.
- getRight() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the right sequence of this derivative.
- getRight() - Method in class de.citec.tcs.alignment.SoftDTWModel
-
Returns the right sequence of this derivative.
- getRight() - Method in class de.citec.tcs.alignment.SoftPathModel
-
Returns the right sequence of this derivative.
- getRoundedString(double, int) - Static method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
-
Returns the string representation of the given number to the given
precision.
- getRules() - Method in class de.citec.tcs.alignment.adp.FlexibleGrammar
-
Returns all production rules that are stored in this grammar.
- getScore() - Method in class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm.ScoreEntry
-
- getScore() - Method in class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- getScore() - Method in class de.citec.tcs.alignment.StrictAlignmentScoreAlgorithm.ScoreEntry
-
- getScore() - Method in class de.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getScores() - Method in class de.citec.tcs.alignment.PathMap
-
Get all scores for which paths exist within this map.
- getSequence() - Method in class de.citec.tcs.alignment.sequence.Node
-
Returns the sequence this node belongs to.
- getSequences() - Method in class de.citec.tcs.alignment.ParallelProcessingEngine
-
- getSigma() - Method in class de.citec.tcs.alignment.comparators.DTWKernelComparator
-
- getSimilarityMatrix() - Method in class de.citec.tcs.alignment.SoftDTWModel
-
This is the dynamic programming matrix calculated by a
DynamicTimeWarpingAlgorithm.
- getSimilarityScore() - Method in class de.citec.tcs.alignment.SoftDTWModel
-
Returns the softDTW score between the two input sequences.
- getSize() - Method in class de.citec.tcs.alignment.PathMap
-
Returns the number of paths stored in this map.
- getSkipDeleteComparison() - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Returns the comparison value that is used to compute the cost of
skip-deletions if the dynamic flag is set to true.
- getSkipDeletionCost(String) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- getSkipDeletionCost() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
Returns the (constant) cost for deleting a value using a skip.
- getSkipDeletionCosts() - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns all skip deletion costs without any other costs.
- getSkipDeletionMatrix() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the vector of skip-deletion costs.
- getSkipDeletionMatrix() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the vector of skip-deletion costs.
- getSkipFactor() - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Returns the cost factor for skipDeletions and skipInsertions for
a dynamic comparison.
- getSkipInsertComparison() - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Returns the comparison value that is used to compute the cost of
skip-insertions if the dynamic flag is set to true.
- getSkipInsertionCost(String) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- getSkipInsertionCost() - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
Returns the (constant) cost for inserting a value using a skip.
- getSkipInsertionCosts() - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns all skip insertion costs without any other costs.
- getSkipInsertionMatrix() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the vector of skip-insertion costs.
- getSkipInsertionMatrix() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the vector of skip-insertion costs.
- getSoftmin() - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getSpecification() - Method in class de.citec.tcs.alignment.AbstractAffineAlignmentAlgorithm
-
This should return the specification that is used for this Algorithm.
- getSpecification() - Method in class de.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This should return the specification that is used for this Algorithm.
- getSpecification() - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
-
This should return the specification that is used for this Algorithm.
- getSpecification() - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
-
This should return the specification that is used for this Algorithm.
- getSpecification() - Method in class de.citec.tcs.alignment.adp.SoftADPPathModel
-
Returns the AlignmentSpecification that was used to compute this
SoftAffinePathModel.
- getSpecification() - Method in interface de.citec.tcs.alignment.AlignmentAlgorithm
-
This should return the specification that is used for this Algorithm.
- getSpecification() - Method in class de.citec.tcs.alignment.KernelDTWFullAlgorithm
-
- getSpecification() - Method in class de.citec.tcs.alignment.SoftAffinePathModel
-
Returns the AlignmentSpecification that was used to compute this
SoftAffinePathModel.
- getSpecification() - Method in class de.citec.tcs.alignment.SoftPathModel
-
Returns the AlignmentSpecification that was basis for this Alignment.
- getSpecificationClass() - Method in enum de.citec.tcs.alignment.sequence.ValueType
-
Returns the corresponding specification class for this ValueType.
- getSpecificaton() - Method in class de.citec.tcs.alignment.AlignmentPath
-
- getSpecificaton() - Method in class de.citec.tcs.alignment.SoftDTWModel
-
Returns the AlignmentSpecification that was basis for this Alignment.
- getSteps() - Method in class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
-
Returns the number of steps that already have been completed.
- getSteps() - Method in interface de.citec.tcs.alignment.parallel.ProgressReporter
-
Returns the number of steps that already have been completed.
- getString() - Method in class de.citec.tcs.alignment.sequence.StringValue
-
Returns the actual string.
- getSymbol(int) - Method in class de.citec.tcs.alignment.sequence.Alphabet
-
This is equivalent to "getKeyword"
- getSymbol() - Method in class de.citec.tcs.alignment.sequence.SymbolicValue
-
Returns this actual symbol.
- getSymbolIndex(String) - Method in class de.citec.tcs.alignment.sequence.Alphabet
-
This is equivalent to "getKeywordIndex"
- getSymbols() - Method in class de.citec.tcs.alignment.sequence.Alphabet
-
This is equivalent to "getKeywords"
- getTabSize() - Method in class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
Returns as how many characters a tab should be counted.
- getTotalSteps() - Method in class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
-
Returns the total number of steps that are necessary to complete the
overall task.
- getTotalSteps() - Method in interface de.citec.tcs.alignment.parallel.ProgressReporter
-
Returns the total number of steps that are necessary to complete the
overall task.
- getType() - Method in class de.citec.tcs.alignment.comparators.CharStatComparator
- getType() - Method in interface de.citec.tcs.alignment.comparators.Comparator
-
- getType() - Method in class de.citec.tcs.alignment.comparators.DTWKernelComparator
-
- getType() - Method in class de.citec.tcs.alignment.comparators.EuclideanComparator
- getType() - Method in class de.citec.tcs.alignment.comparators.L1NormComparator
- getType() - Method in class de.citec.tcs.alignment.comparators.NCDComparator
- getType() - Method in class de.citec.tcs.alignment.comparators.ReplacementComparator
- getType() - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
- getType() - Method in class de.citec.tcs.alignment.comparators.ZeroNormComparator
- getType() - Method in class de.citec.tcs.alignment.Operation
-
- getType() - Method in class de.citec.tcs.alignment.sequence.AbstractValue
-
Returns the type of this value.
- getType() - Method in class de.citec.tcs.alignment.sequence.KeywordSpecification
-
Returns the specified type for that keyword.
- getType() - Method in interface de.citec.tcs.alignment.sequence.Value
-
Returns the type of this value.
- getValue() - Method in class de.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- getValue(String) - Method in class de.citec.tcs.alignment.sequence.Node
-
Returns the value stored in this Node for the given keyword or null of no
value is stored for the given keyword in this node.
- getValue(int) - Method in class de.citec.tcs.alignment.sequence.Node
-
Returns the value stored in this Node for the given keyword or null of no
value is stored for the given keyword in this node.
- getValueClass() - Method in enum de.citec.tcs.alignment.sequence.ValueType
-
The corresponding class of this ValueType.
- getVector() - Method in class de.citec.tcs.alignment.sequence.VectorialValue
-
Returns the actual vector.
- getVisualizationData(AlignmentPath) - Method in class de.citec.tcs.alignment.visualization.AbstractVisualizer
-
Returns the visualization as string.
- getWeightedLocalCost() - Method in class de.citec.tcs.alignment.Operation
-
- getWeighting() - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
Returns the current keyword weighting.
- getWeighting() - Method in class de.citec.tcs.alignment.PathMap
-
Returns the weighting that is used during derivative calculation.
- getWeightThreshold() - Method in class de.citec.tcs.alignment.AbstractAffineAlignmentAlgorithm
-
- getWeightThreshold() - Method in class de.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
- getWeightThreshold() - Method in class de.citec.tcs.alignment.AbstractStrictDTWAlgorithm
-
- getWeightThreshold() - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
-
- GlobalAsymmetricGrammar - Class in de.citec.tcs.alignment.adp
-
This is a slight variation of the global alignment grammar.
- GlobalAsymmetricGrammar() - Constructor for class de.citec.tcs.alignment.adp.GlobalAsymmetricGrammar
-
Creates an instance of the global, asymmetric grammar.
- GlobalAsymmetricGrammar.Nonterminal - Enum in de.citec.tcs.alignment.adp
-
- GlobalGrammar - Class in de.citec.tcs.alignment.adp
-
This is the most basic (and classic) alignment grammar there is.
- GlobalGrammar() - Constructor for class de.citec.tcs.alignment.adp.GlobalGrammar
-
This creates an instance of the global alignment grammar.
- GlobalGrammar.Nonterminal - Enum in de.citec.tcs.alignment.adp
-
- Grammar<N extends Enum<N>> - Interface in de.citec.tcs.alignment.adp
-
An Algebraic Dynamic Programming (ADP) grammar is a regular tree
grammar.
- GrammarValidityException - Exception in de.citec.tcs.alignment.adp
-
This exception is thrown if a flexible grammar is invalid.
- GrammarValidityException(String) - Constructor for exception de.citec.tcs.alignment.adp.GrammarValidityException
-
- ScoreBasedWeighting - Enum in de.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.citec.tcs.alignment.sequence
-
Usually a sequence for alignments is defined as a sequence of symbols.
- Sequence(NodeSpecification) - Constructor for class de.citec.tcs.alignment.sequence.Sequence
-
Sets up an empty sequence with the given NodeSpecification as basis.
- Sequence(String) - Constructor for class de.citec.tcs.alignment.sequence.Sequence
-
Sets up a trivial sequence with only one keyword (DEFAULTKEYWORD) and treats
the string content between | delimiters in the input string as symbolic
values.
- Sequence(String, Alphabet) - Constructor for class de.citec.tcs.alignment.sequence.Sequence
-
Sets up a trivial sequence with only one keyword (DEFAULTKEYWORD) and treats
the string content between | delimiters in the input string as symbolic
values.
- set(int, int, X) - Method in class de.citec.tcs.alignment.SparseMatrix
-
Sets the value at the given position in the matrix.
- setAlpha(double) - Method in class de.citec.tcs.alignment.comparators.HyperbolicNormalizer
-
- setApproxThreshold(double) - Method in class de.citec.tcs.alignment.adp.SoftADPFullAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- setApproxThreshold(double) - Method in class de.citec.tcs.alignment.adp.SoftADPScoreAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- setApproxThreshold(double) - Method in class de.citec.tcs.alignment.SoftAffineAlignmentFullAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- setApproxThreshold(double) - Method in class de.citec.tcs.alignment.SoftAffineAlignmentScoreAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- setApproxThreshold(double) - Method in class de.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
Sets the threshold for which exponents within the softmin function will
be disregarded.
- setApproxThreshold(double) - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
Sets the threshold for which exponents within the softmin function will
be disregarded.
- setApproxThreshold(double) - Method in class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
For more information on the ApproxThreshold have a look at the
Softmin class.
- setBeta(double) - Method in class de.citec.tcs.alignment.adp.SoftADPFullAlgorithm
-
- setBeta(double) - Method in class de.citec.tcs.alignment.adp.SoftADPScoreAlgorithm
-
Sets the parameter defining the "softness" of the alignment.
- setBeta(double) - Method in class de.citec.tcs.alignment.comparators.ExponentialNormalizer
-
- setBeta(double) - Method in class de.citec.tcs.alignment.SoftAffineAlignmentFullAlgorithm
-
Sets the parameter defining the "softness" of the alignment.
- setBeta(double) - Method in class de.citec.tcs.alignment.SoftAffineAlignmentScoreAlgorithm
-
Sets the parameter defining the "softness" of the alignment.
- setBeta(double) - Method in class de.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
- setBeta(double) - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
- setBeta(double) - Method in class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
- setCancelOnException(boolean) - Method in class de.citec.tcs.alignment.parallel.Engine
-
Sets a flag that decides whether this Engine stops computation if one
thread
throws an exception.
- setComparator(String, Comparator) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
Sets the comparator for a given keyword.
- setComparator(int, Comparator) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
Sets the comparator for a given keyword.
- setComparatorDistances(double[]) - Method in class de.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.citec.tcs.alignment.comparators.NCDComparator
-
- setCostMatrix(ReplacementCosts) - Method in class de.citec.tcs.alignment.comparators.ReplacementComparator
-
Sets the ReplacementCosts that shall be used within this Comparator.
- setCostMatrix(double[][]) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets the cost matrix itself.
- setDecimalPlaces(int) - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
-
This specifies how many decimal places (after comma) should be
visualized.
- setDelCosts(double[]) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setDeleteComparison(V) - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Sets the comparison value that is used to compute the cost of
deletions if the dynamic flag is set to true.
- setDeletionCost(String, double) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- setDeletionCost(double) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
Sets the (constant) cost for deleting a value.
- setDeletionCosts(double[]) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets all deletion costs without any other costs.
- setDelLocal(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setDelProb(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setDelSoftDerivative(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setDynamic(boolean) - Method in class de.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.
- setEndExclusive(boolean) - Method in class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
Sets if the end column of each given codePosition should be in-
or excluded in the visualization.
- setFull() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Clears all current calculation tasks and instead adds a task for every
matrix entry, such that the full matrix is calculated on the next call of
the "calculate" method.
- setInsCosts(double[]) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setInsertComparison(V) - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Sets the comparison value that is used to compute the cost of
insertions if the dynamic flag is set to true.
- setInsertionCost(String, double) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- setInsertionCost(double) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
Sets the (constant) cost for inserting a value.
- setInsertionCosts(double[]) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets all insertion costs without any other costs.
- setInsLocal(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setInsProb(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setInsSoftDerivative(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setMatchCost(double) - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
-
Sets the cost for matches (0 per default).
- setMax(double) - Method in class de.citec.tcs.alignment.comparators.AffineNormalizer
-
Sets the maximum possible value, which will be mapped to 1.
- setMin(double) - Method in class de.citec.tcs.alignment.comparators.AffineNormalizer
-
Sets the minimum possible value, which will be mapped to 0.
- setMinMiddleSkips(int) - Method in class de.citec.tcs.alignment.AbstractAffineAlignmentAlgorithm
-
The minimum number of skips that have to be done in the middle
of an alignment.
- setMismatchCost(double) - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
-
Sets the cost for mismatches (1 per default).
- setNormalizer(Normalizer) - Method in class de.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.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.citec.tcs.alignment.parallel.Engine
-
Sets the number of threads that are used for computation (16 per
default).
- setPathLimit(int) - Method in class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
This sets the number of paths that shall be sampled.
- setPathLimit(int) - Method in class de.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.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.
- setPreferredCooptimal(OperationType[]) - Method in class de.citec.tcs.alignment.StrictAffineAlignmentFullAlgorithm
-
This allows to specify an order in which operations shall be preferred if
cooptimal alignments occur.
- setProgressReportStepSize(double) - Method in class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
-
Sets the percent of computation that have to be completed until a new
notification is written to the command line.
- setRepCosts(double[]) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setReplacementCost(String, String, double) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- setReplacementCosts(double[][]) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets the whole matrix of replacement costs without gap and skip costs.
- setRepLocal(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setReporter(ProgressReporter) - Method in class de.citec.tcs.alignment.parallel.Engine
-
Sets the ProgressReporter that is used to report progress.
- setRepProb(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setRepSoftDerivative(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setRestrictKeywords(boolean) - Method in class de.citec.tcs.alignment.visualization.HTMLVisualizer
-
If this flag is set to "true" the HTMLVisualizer will only print out
table columns for the keywords specified in "keywords".
- setSkipDeleteComparison(V) - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Sets the comparison value that is used to compute the cost of
skip-deletions if the dynamic flag is set to true.
- setSkipDeletionCost(String, double) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- setSkipDeletionCost(double) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
Sets the (constant) cost for deleting a value using a skip.
- setSkipDeletionCosts(double[]) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets all skip deletion costs without any other costs.
- setSkipFactor(double) - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Sets the cost factor for skipDeletions and skipInsertions for
a dynamic comparison.
- setSkipInsertComparison(V) - Method in class de.citec.tcs.alignment.comparators.ComparisonBasedSkipExtendedComparator
-
Sets the comparison value that is used to compute the cost of
skip-insertions if the dynamic flag is set to true.
- setSkipInsertionCost(String, double) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- setSkipInsertionCost(double) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
Sets the (constant) cost for inserting a value using a skip.
- setSkipInsertionCosts(double[]) - Method in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets all skip insertion costs without any other costs.
- setSoftmin(double) - Method in class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setSpecificTasks(boolean[][]) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Clears all current calculation tasks and instead adds a task for every
matrix entry that is set to "true" in the given boolean matrix.
- setSpecificTasks(MatrixEngine.MatrixCoordinate[]) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Clears all current calculation tasks and instead adds a task for every
given matrix coordinate.
- setSpecificTasks(Collection<MatrixEngine.MatrixCoordinate>) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Clears all current calculation tasks and instead adds a task for every
given matrix coordinate.
- setSpecificTasks(int[][]) - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Clears all current calculation tasks and instead adds a task for every
given matrix coordinate.
- setString(String) - Method in class de.citec.tcs.alignment.sequence.StringValue
-
- setSymbol(String) - Method in class de.citec.tcs.alignment.sequence.SymbolicValue
-
Sets the actual symbol.
- setSymmetric() - Method in class de.citec.tcs.alignment.parallel.MatrixEngine
-
Clears all current calculation tasks and instead adds a task for every
matrix entry in the upper half of the matrix.
- setTabSize(int) - Method in class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
This manipulates as how many characters a tab should be
counted.
- setTotalSteps(int) - Method in class de.citec.tcs.alignment.parallel.CommandLineProgressReporter
-
Sets the total number of steps that are necessary to complete the overall
task.
- setTotalSteps(int) - Method in interface de.citec.tcs.alignment.parallel.ProgressReporter
-
Sets the total number of steps that are necessary to complete the overall
task.
- setUpSpecification(Sequence[]) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
-
Sets up a default AlignmentSpecification for the simple
StringEditDistance problem.
- setUpSpecification(Sequence[], double, double, double) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
-
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
- setUpSpecification(Sequence[], double[][]) - Static method in class de.citec.tcs.alignment.wrappers.StringEditDistance
-
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
- setUpSpecification(Sequence[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
-
Sets up an AlignmentSpecification for an array of vectorial sequences.
- setUpSpecification(Sequence[], GapComparator<VectorialValue>) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
-
Sets up an AlignmentSpecification for an array of vectorial sequences.
- setUpSpecification(Sequence[], GapComparator[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
-
Sets up an AlignmentSpecification for an array of vectorial sequences.
- setUpSpecification(Sequence[], double[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
-
Sets up an AlignmentSpecification for an array of vectorial sequences.
- setUpSpecification(Sequence[], GapComparator<VectorialValue>, double[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
-
Sets up an AlignmentSpecification for an array of vectorial sequences.
- setUpSpecification(Sequence[], GapComparator[], double[]) - Static method in class de.citec.tcs.alignment.wrappers.VectorialSequences
-
Sets up an AlignmentSpecification for an array of vectorial sequences.
- setValue(Double) - Method in class de.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- setValue(String, Value) - Method in class de.citec.tcs.alignment.sequence.Node
-
Sets the value for the given keyword.
- setValue(int, Value) - Method in class de.citec.tcs.alignment.sequence.Node
-
Sets the value for the given keyword.
- setVector(double[]) - Method in class de.citec.tcs.alignment.sequence.VectorialValue
-
Sets the actual vector.
- setVector(Object) - Method in class de.citec.tcs.alignment.sequence.VectorialValue
-
Sets the actual vector.
- setWeighting(double[]) - Method in class de.citec.tcs.alignment.AlignmentSpecification
-
This sets the current weighting of keywords.
- setWeighting(ScoreBasedWeighting) - Method in class de.citec.tcs.alignment.PathMap
-
Sets the weighting that is used during derivative calculation.
- setWeightThreshold(double) - Method in class de.citec.tcs.alignment.AbstractAffineAlignmentAlgorithm
-
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.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.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.
- setWeightThreshold(double) - Method in class de.citec.tcs.alignment.adp.AbstractADPAlgorithm
-
Set a weight threshold (between 0 and 1) that determines which keywords
should be ignored during calculation because their weight is negligible.
- size() - Method in class de.citec.tcs.alignment.sequence.IndexingScheme
-
Returns the number of mapped keywords.
- SkipAlignmentAlgorithm<R> - Interface in de.citec.tcs.alignment
-
This is an interface for GapAlignmentAlgorithms that also use skips
(SkipDeletion, SkipInsertion) and in that way are local distance measures.
- SkipComparator<X extends Value> - Interface in de.citec.tcs.alignment.comparators
-
This further specifies the AlignmentComparator to include skips.
- SKIPDEFAULT - Static variable in class de.citec.tcs.alignment.comparators.ReplacementCosts
-
- skipDelete(V) - Method in class de.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.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.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.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.citec.tcs.alignment.comparators
-
This is an abstract class to be used for Comparators that are only
to be used for comparisons per se but can be extended for use with
gaps and skips.
- SkipExtendedComparator() - Constructor for class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
- skipInsert(V) - Method in class de.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.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.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.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.
- SoftADPFullAlgorithm<N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
-
This algorithm returns a SoftADPPathModel based on the given grammar
and algebra/AlignmentSpecification.
- SoftADPFullAlgorithm(Grammar<N>, AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.adp.SoftADPFullAlgorithm
-
Creates a new SoftFullAlgorithm based on the given ADP grammar
and the given AlignmentSpecification/algebra.
- SoftADPPathModel<N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
-
This is basically a large storage class for all results of a
SoftADPFullAlgorithm to facilitate derivative calculation.
- SoftADPPathModel(AlignmentSpecification, Grammar<N>, double, double, double, EnumMap<N, double[][]>, double[][], double[], double[], double[], double[], Sequence, Sequence) - Constructor for class de.citec.tcs.alignment.adp.SoftADPPathModel
-
- SoftADPScoreAlgorithm<N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
-
This algorithm calculates the soft alignment score for the given
input grammar and algebra/AlignmentSpecification.
- SoftADPScoreAlgorithm(Grammar<N>, AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.adp.SoftADPScoreAlgorithm
-
- SoftAffineAlignmentFullAlgorithm - Class in de.citec.tcs.alignment
-
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
- SoftAffineAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.SoftAffineAlignmentFullAlgorithm
-
- SoftAffineAlignmentScoreAlgorithm - Class in de.citec.tcs.alignment
-
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
- SoftAffineAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.SoftAffineAlignmentScoreAlgorithm
-
- SoftAffinePathModel - Class in de.citec.tcs.alignment
-
This is basically a storage for the DP matrix of the
SoftAffineAlignmentAlgorithm.
- SoftAffinePathModel(double, AlignmentSpecification, int, double, EnumMap<AbstractAffineAlignmentAlgorithm.Recurrence, double[][]>, double[][], double[], double[], double[], double[], Sequence, Sequence) - Constructor for class de.citec.tcs.alignment.SoftAffinePathModel
-
- SoftAlignmentFullAlgorithm - Class in de.citec.tcs.alignment
-
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
- SoftAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- SoftAlignmentSamplingAlgorithm - Class in de.citec.tcs.alignment
-
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
- SoftAlignmentSamplingAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- SoftAlignmentScoreAlgorithm - Class in de.citec.tcs.alignment
-
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
- SoftAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- SoftAlignmentScoreAlgorithm.ScoreEntry - Class in de.citec.tcs.alignment
-
- SoftAlignmentScoreAlgorithm.ScoreEntry(double) - Constructor for class de.citec.tcs.alignment.SoftAlignmentScoreAlgorithm.ScoreEntry
-
- SoftDTWModel - Class in de.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.citec.tcs.alignment.SoftDTWModel
-
- Softmin - Class in de.citec.tcs.alignment
-
This implements utility functions for the softmin function.
- Softmin() - Constructor for class de.citec.tcs.alignment.Softmin
-
- softmin(double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
-
This calculates softmin for the given input and the given value
of beta.
- softmin(double, double, double[]) - Static method in class de.citec.tcs.alignment.Softmin
-
This calculates softmin for the given input and the given value
of beta.
- SoftPathModel - Class in de.citec.tcs.alignment
-
This is the soft pendant to the AlignmentPath.
- SoftPathModel(AlignmentSpecification, Sequence, Sequence, double, double, SoftPathModel.SoftMatrixEntry[][]) - Constructor for class de.citec.tcs.alignment.SoftPathModel
-
- SoftPathModel.SoftMatrixEntry - Class in de.citec.tcs.alignment
-
- SoftPathModel.SoftMatrixEntry() - Constructor for class de.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- SourceCodeColumn - Class in de.citec.tcs.alignment.visualization
-
This special HTML column allows users to visualize source code, given that
you have put the information on the location into the Sequence, meaning that
your NodeSpecification has two keywords, one specifying the path to the
respective code file and one specifying the position within that code file.
- SourceCodeColumn(String, String, String, String) - Constructor for class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
- SourceCodeColumn(String, String, String) - Constructor for class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
- SourceCodeColumn(String, String) - Constructor for class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
- sparseComparisonDerivative(StringValue, StringValue) - Method in class de.citec.tcs.alignment.comparators.CharStatComparator
-
This should implement the local derivative calculation in case of
comparisons.
- sparseComparisonDerivative(VectorialValue, VectorialValue) - Method in class de.citec.tcs.alignment.comparators.EuclideanComparator
-
This should implement the local derivative calculation in case of
comparisons.
- sparseComparisonDerivative(VectorialValue, VectorialValue) - Method in class de.citec.tcs.alignment.comparators.L1NormComparator
-
This should implement the local derivative calculation in case of
comparisons.
- sparseComparisonDerivative(StringValue, StringValue) - Method in class de.citec.tcs.alignment.comparators.NCDComparator
-
This should implement the local derivative calculation in case of
comparisons.
- sparseComparisonDerivative(V, V) - Method in class de.citec.tcs.alignment.comparators.SkipExtendedComparator
-
This should implement the local derivative calculation in case of
comparisons.
- sparseComparisonDerivative(SymbolicValue, SymbolicValue) - Method in class de.citec.tcs.alignment.comparators.TrivialEditComparator
-
This should implement the local derivative calculation in case of
comparisons.
- sparseComparisonDerivative(VectorialValue, VectorialValue) - Method in class de.citec.tcs.alignment.comparators.ZeroNormComparator
-
This should implement the local derivative calculation in case of
comparisons.
- SparseDerivableComparator<X extends Value,Y> - Interface in de.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.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.citec.tcs.alignment.comparators
-
- SparseLocalDerivative.EmptySparseLocalEntry() - Constructor for class de.citec.tcs.alignment.comparators.SparseLocalDerivative.EmptySparseLocalEntry
-
- SparseLocalDerivative.FixedSparseLocalDerivative - Class in de.citec.tcs.alignment.comparators
-
This implements the SparseLocalDerivative interface for a fixed number of
entries.
- SparseLocalDerivative.FixedSparseLocalDerivative(int) - Constructor for class de.citec.tcs.alignment.comparators.SparseLocalDerivative.FixedSparseLocalDerivative
-
- SparseLocalDerivative.FlexibleSparseLocalDerivative - Class in de.citec.tcs.alignment.comparators
-
- SparseLocalDerivative.FlexibleSparseLocalDerivative() - Constructor for class de.citec.tcs.alignment.comparators.SparseLocalDerivative.FlexibleSparseLocalDerivative
-
- SparseLocalDerivative.SparseDeriativeEntry - Class in de.citec.tcs.alignment.comparators
-
- SparseLocalDerivative.SparseDeriativeEntry(int, double) - Constructor for class de.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- SparseLocalDerivative.TrivialSparseLocalDerivative - Class in de.citec.tcs.alignment.comparators
-
This is a representation with just one entry.
- SparseLocalDerivative.TrivialSparseLocalDerivative() - Constructor for class de.citec.tcs.alignment.comparators.SparseLocalDerivative.TrivialSparseLocalDerivative
-
- SparseMatrix<X> - Class in de.citec.tcs.alignment
-
This models a sparse matrix that does not have to be fully calculated.
- SparseMatrix() - Constructor for class de.citec.tcs.alignment.SparseMatrix
-
- SRC_LIMIT - Static variable in class de.citec.tcs.alignment.visualization.SourceCodeColumn
-
- STDKEYWORD - Static variable in class de.citec.tcs.alignment.wrappers.VectorialSequences
-
- StrictADPFullAlgorithm<N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
-
This algorithm calculates an optimal AlignmentPath using the given
ADP grammar and algebra/AlignmentSpecification.
- StrictADPFullAlgorithm(Grammar<N>, AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.adp.StrictADPFullAlgorithm
-
- StrictADPScoreAlgorithm<N extends Enum<N>> - Class in de.citec.tcs.alignment.adp
-
This algorithm calculates the strict alignment score for the given
input grammar and algebra/AlignmentSpecification.
- StrictADPScoreAlgorithm(Grammar<N>, AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.adp.StrictADPScoreAlgorithm
-
- StrictAffineAlignmentFullAlgorithm - Class in de.citec.tcs.alignment
-
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
- StrictAffineAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.StrictAffineAlignmentFullAlgorithm
-
- StrictAffineAlignmentScoreAlgorithm - Class in de.citec.tcs.alignment
-
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
- StrictAffineAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.StrictAffineAlignmentScoreAlgorithm
-
- StrictAlignmentFullAlgorithm - Class in de.citec.tcs.alignment
-
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
- StrictAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- StrictAlignmentFullAlgorithm.FullMatrixEntry - Class in de.citec.tcs.alignment
-
- StrictAlignmentFullAlgorithm.FullMatrixEntry(double, int, int, StrictAlignmentFullAlgorithm.FullMatrixEntry) - Constructor for class de.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- StrictAlignmentScoreAlgorithm - Class in de.citec.tcs.alignment
-
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
- StrictAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- StrictAlignmentScoreAlgorithm.ScoreEntry - Class in de.citec.tcs.alignment
-
- StrictAlignmentScoreAlgorithm.ScoreEntry(double) - Constructor for class de.citec.tcs.alignment.StrictAlignmentScoreAlgorithm.ScoreEntry
-
- StrictAllOptimalAlgorithm - Class in de.citec.tcs.alignment
-
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
- StrictAllOptimalAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.StrictAllOptimalAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- StrictAllOptimalAlgorithm.FullMatrixEntry - Class in de.citec.tcs.alignment
-
- StrictAllOptimalAlgorithm.FullMatrixEntry(double, double, double, double, int, int) - Constructor for class de.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- StrictDTWFullAlgorithm - Class in de.citec.tcs.alignment
-
This is an implementation of the AbstractStrictDTWAlgorithm to
calculate just one exemplary optimal DTW path.
- StrictDTWFullAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.StrictDTWFullAlgorithm
-
- StrictDTWScoreAlgorithm - Class in de.citec.tcs.alignment
-
This is an implementation of the AbstractStrictDTWAlgorithm to
calculate just the score.
- StrictDTWScoreAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.StrictDTWScoreAlgorithm
-
- StrictKPathAlgorithm - Class in de.citec.tcs.alignment
-
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
- StrictKPathAlgorithm(AlignmentSpecification) - Constructor for class de.citec.tcs.alignment.StrictKPathAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- StrictKPathAlgorithm.IndexedStochasticPriorityQueue<K extends Comparable<K>,V> - Class in de.citec.tcs.alignment
-
This is a helper class, which actually extends the TreeMap to implement a
PriorityQueue that is able to poll the minimum as well as the maximum in
constanst time.
- StrictKPathAlgorithm.IndexedStochasticPriorityQueue() - Constructor for class de.citec.tcs.alignment.StrictKPathAlgorithm.IndexedStochasticPriorityQueue
-
- StringEditDistance - Class in de.citec.tcs.alignment.wrappers
-
This is a simple wrapper to support an easier interface for the simple
StringEditDistance problem.
- StringEditDistance() - Constructor for class de.citec.tcs.alignment.wrappers.StringEditDistance
-
- StringKeywordSpecification - Class in de.citec.tcs.alignment.sequence
-
This specifies String keywords which are not especially restricted.
- StringKeywordSpecification(String) - Constructor for class de.citec.tcs.alignment.sequence.StringKeywordSpecification
-
- StringValue - Class in de.citec.tcs.alignment.sequence
-
This value is supposed to represent strings that are not restricted to a
certain alphabet.
- StringValue() - Constructor for class de.citec.tcs.alignment.sequence.StringValue
-
- StringValue(String) - Constructor for class de.citec.tcs.alignment.sequence.StringValue
-
- StringVisualizer - Class in de.citec.tcs.alignment.visualization
-
This is a trivial Visualizer that just calls the toString() method of
AlignmentPath.
- StringVisualizer() - Constructor for class de.citec.tcs.alignment.visualization.StringVisualizer
-
- SymbolicKeywordSpecification - Class in de.citec.tcs.alignment.sequence
-
This specifies symbolic keywords by their alphabet.
- SymbolicKeywordSpecification(Alphabet, String) - Constructor for class de.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
-
- SymbolicValue - Class in de.citec.tcs.alignment.sequence
-
This is a special value class that is restricted to a finite list of values
defined by an alphabet.
- SymbolicValue(Alphabet) - Constructor for class de.citec.tcs.alignment.sequence.SymbolicValue
-
- SymbolicValue(Alphabet, String) - Constructor for class de.citec.tcs.alignment.sequence.SymbolicValue
-