- calc_weighted_comp_sum(Comparator[], double[], int[], Node, Node) - Static method in class de.unibi.citec.tcs.alignment.SoftDTWModel
-
Returns weighted sum k of local comparators: k = sum(w_i * k_i) with:
k_i: local comparators w_i: local weights
Note: Comparators, weights, originalIndices are supposed to originate
from the same AlignmentSpecification.
- calculate() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
This starts the calculation of the pairwise alignment of the input
Sequencs according to the given algorithm.
- calculateAlignment(Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This calculates the alignment between the Sequences a and b and returns
it as an instance of the result class for this algorithm.
- calculateAlignment(Sequence, Sequence) - Method in interface de.unibi.citec.tcs.alignment.AlignmentAlgorithm
-
This calculates the alignment between the Sequences a and b and returns
it as an instance of the result class for this algorithm.
- calculateAlignment(Sequence, Sequence) - Method in class de.unibi.citec.tcs.alignment.DynamicTimeWarpingAlgorithm
-
This calculates the alignment between the Sequences a and b and returns
it as an instance of the result class for this algorithm.
- calculateComparatorDerivatives(DerivableComparator<?, R>) - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
-
- calculateDeletionCosts(Node, AlignmentSpecification) - Static method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This calculates the non-weighted costs for deleting the single values in
node a.
- calculateDerivative(AlignmentAlgorithm<? extends AlignmentDerivativeAlgorithm>, Sequence, Sequence) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
-
Calculates the alignment derivative between the two given input sequences
using the given algorithm.
- calculateDerivatives(AlignmentAlgorithm<R>, Sequence[], int) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
-
Calculates the pairwise alignment derivative between all given input
sequences using the given algorithm.
- calculateInsertionCosts(Node, AlignmentSpecification) - Static method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This calculates the non-weighted costs for inserting the single values of
node b.
- calculateLocalDerivative(int, X, X, OperationType) - Method in interface de.unibi.citec.tcs.alignment.comparators.DerivableComparator
-
This is called by an AlignmentDerivativeAlgorithm and should calculate
the local derivative for only one comparison of the values a and b.
- calculateLocalDerivative(int, VectorialValue, VectorialValue, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
-
TODO: think about opterationType
This is called by an AlignmentDerivativeAlgorithm and should calculate
the local derivative for only one comparison of the values a and b.
- calculateLocalDerivative(int, SymbolicValue, SymbolicValue, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
-
This is called by an AlignmentDerivativeAlgorithm and should calculate
the local derivative for only one comparison of the values a and b.
- calculateLocalDerivative(int, SymbolicValue, SymbolicValue, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
This is called by an AlignmentDerivativeAlgorithm and should calculate
the local derivative for only one comparison of the values a and b.
- calculateParameterDerivative(DerivableComparator<X, Y>) - Method in interface de.unibi.citec.tcs.alignment.AlignmentDerivativeAlgorithm
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.PathList
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.PathMap
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateRawParameterDerivative(DerivableComparator<X, Y>) - Method in interface de.unibi.citec.tcs.alignment.AlignmentDerivativeAlgorithm
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateRawParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateRawParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.PathList
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateRawParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.PathMap
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateRawParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateRawParameterDerivative(DerivableComparator<X, Y>) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
-
This returns the derivatives for all parameters of the given comparator
according to the implementation.
- calculateReplacementCosts(Node, Node, AlignmentSpecification) - Static method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This calculates the non-weighted costs for replacing the single values in
node a by the values in node b.
- calculateSparseLocalDerivative(SymbolicValue, SymbolicValue, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
-
This method shall return a sparse representation of the derivative for
all parameters that have non-zero derivatives in this step of the
alignment.
- calculateSparseLocalDerivative(X, X, OperationType) - Method in interface de.unibi.citec.tcs.alignment.comparators.SparseDerivableComparator
-
This method shall return a sparse representation of the derivative for
all parameters that have non-zero derivatives in this step of the
alignment.
- calculateSparseLocalDerivative(SymbolicValue, SymbolicValue, OperationType) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
This method shall return a sparse representation of the derivative for
all parameters that have non-zero derivatives in this step of the
alignment.
- calculateWeightDerivative() - Method in interface de.unibi.citec.tcs.alignment.AlignmentDerivativeAlgorithm
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.PathList
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.PathMap
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
-
Calculates the derivative for each keyword weight.
- calculateWeightDerivatives() - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
-
This calculates the weight derivatives for each of the input
AlignmentDerivativeAlgorithms.
- calculateWeighting(Collection<Double>) - Method in enum de.unibi.citec.tcs.alignment.ScoreBasedWeighting
-
- calculateWeighting(double[]) - Method in enum de.unibi.citec.tcs.alignment.ScoreBasedWeighting
-
This calculates the normalized weights (between 0 and 1 and adding up
to 1) for the given scores.
- CharStatComparator - Class in de.unibi.citec.tcs.alignment.comparators
-
This compares strings using statistics over the number of letters inside.
- CharStatComparator() - Constructor for class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
-
- CharStatComparator(Normalizer) - Constructor for class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
-
- CLASSNAME_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
-
- clone() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
- CODEPOSITION_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
-
- Comparator<X extends Value> - Interface in de.unibi.citec.tcs.alignment.comparators
-
This defines a function that returns a normalized distance between two
objects.
- compare(StringValue, StringValue) - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
-
This has to return a distance between a and b with the following
restrictions:
The return value has to lie between 0 and 1.
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.unibi.citec.tcs.alignment.comparators.Comparator
-
This has to return a distance between a and b with the following
restrictions:
The return value has to lie between 0 and 1.
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.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
-
This has to return a distance between a and b with the following
restrictions:
The return value has to lie between 0 and 1.
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.unibi.citec.tcs.alignment.comparators.EuclidianComparator
-
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.unibi.citec.tcs.alignment.comparators.L1NormComparator
-
This has to return a distance between a and b with the following
restrictions:
The return value has to lie between 0 and 1.
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.unibi.citec.tcs.alignment.comparators.ReplacementComparator
-
This has to return a distance between a and b with the following
restrictions:
The return value has to lie between 0 and 1.
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.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
This has to return a distance between a and b with the following
restrictions:
The return value has to lie between 0 and 1.
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.
- contains(String) - Method in class de.unibi.citec.tcs.alignment.visualization.ExternalContent
-
- createDelInitial(X, int, double) - Method in class de.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This circumvents Javas rule against generic array cration by using
reflection.
- createGenericMatrix(int, int, Class<X>) - Static method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This circumvents Javas rule against generic array cration by using
reflection.
- createHTMLs(AlignmentPath[][], ArrayList<String>, String, String, String[], ExternalContent[], boolean) - Static method in class de.unibi.citec.tcs.alignment.visualization.Visualization
-
Visualizes given alignments in clear and adaptable tables.
- createInitial() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This method should not be called from outside!
The subclass specifies the entry (0,0) of the alignment matrix with this
method.
- createInitial() - Method in class de.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.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.unibi.citec.tcs.alignment
-
This is an interface for Alignment algorithms that use gaps (insertion and
deletion operations) in the alignment.
- GapComparator<X extends Value> - Interface in de.unibi.citec.tcs.alignment.comparators
-
This specifies the comparator interface slightly to include the case that
entities might be deleted/inserted.
- GAPDEFAULT - Static variable in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- get(int, int) - Method in class de.unibi.citec.tcs.alignment.SparseMatrix
-
Returns the value stored at the given position or null if no value was
stored there until now.
- getAlgorithm() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
- getAlgorithms() - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
-
- getAllPaths() - Method in class de.unibi.citec.tcs.alignment.PathMap
-
Returns all paths stored in this map in order of their score (from
good/low to bad/high).
- getAlpha() - Method in class de.unibi.citec.tcs.alignment.comparators.HyperbolicNormalizer
-
- getAlphabet() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- getAlphabet() - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
-
Returns the Alphabet that defines which symbols are allowed for this
keyword.
- getAlphabet() - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
-
Returns the Alphabet that defines which symbols are allowed for this
keyword.
- getApproxThreshold() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
Returns the threshold for which exponents within the softmin function
will be disregarded.
- getApproxThreshold() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
Returns the threshold for which exponents within the softmin function
will be disregarded.
- getAverageScore() - Method in class de.unibi.citec.tcs.alignment.PathList
-
Returns the average score for all paths in this list.
- getBeta() - Method in class de.unibi.citec.tcs.alignment.comparators.ExponentialNormalizer
-
- getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
- getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
- getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
- getBeta() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
-
The parameter defining the "softness" of the alignment.
- getCodeFileContent() - Method in class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
-
Returns codeFileContent, which holds the line-wise content of the
source code files specified by every node.
- getCodeFileContentForKey(String) - Method in class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
-
Returns line-wise content of the specified file.
- getComparator(String) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
-
Returns the Comparator that is currently set for the given keyword.
- getComparator(int) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
-
Returns the Comparator that is currently set for the given keyword.
- getComparatorDistances() - Method in class de.unibi.citec.tcs.alignment.Operation
-
Returns the local costs given by the Comparators specified for this
Alignment to align the left Node in this Operation with the right Node
(or deleting, inserting, skipping nodes respectively).
- getContent(String) - Method in class de.unibi.citec.tcs.alignment.visualization.ExternalContent
-
Returns the external content for a specific keyword.
- getContent(String, int) - Method in class de.unibi.citec.tcs.alignment.visualization.ExternalContent
-
Returns the external content for a specific keyword and index.
- getCostMatrix() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
-
Returns the ReplacementCosts object that defines the explicit cost matrix
for replacements between the symbols in the given alphabet.
- getCostMatrix() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns the cost matrix itself.
- getDefaultComparator() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
If this is a simple string alignment we return the replacement comparator
for the symbols.
- getDefaultComparator() - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
-
This returns a valid Comparator for this KeywordSpecification.
- getDelCosts() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getDeletionCost(String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- getDeletionCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns all deletion costs without any other costs.
- getDelLocal() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getDelLocal() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getDelProb() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getDelSoftDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getDerivative() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- getDoCalculation() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
Please refer to the corresponding setter method for more information.
- getEntryClass() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
Returns the class of matrix entries.
- getFiles() - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
-
Returns the files map.
- getGapComparison() - Method in class de.unibi.citec.tcs.alignment.comparators.EuclidianComparator
-
Please refer to the corresponding setter method for more information.
- getGapComparison() - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
-
Please refer to the corresponding setter method for more information.
- getGapScore() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Returns the score used if a symbol is deleted or inserted.
- getGapString() - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
-
The string that is used as reference to determine the INSERTION/DELETION
cost of another string.
- getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
-
- getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractSpecialHTMLTransformer
-
Transforms the given node into HTML content for the visualization.
- getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.HTImageFromPath
-
Takes an image file from the given node and generates a
corresponding HTML representation.
- getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
-
Takes some code positions from the given node and extracts the
corresponding string from a file specified by 'SourceCodeFile'
in the node.
- getHTMLforNode(Node) - Method in class de.unibi.citec.tcs.alignment.visualization.PartStringFromFileExternalContent
-
- getHTMLforNode(Node) - Method in interface de.unibi.citec.tcs.alignment.visualization.SpecialHTMLTransformer
-
Transforms the given node into HTML content for the visualization.
- getI() - Method in class de.unibi.citec.tcs.alignment.MatrixCoordinate
-
- getI() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- getI() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getInsCosts() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getInsertionCost(String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- getInsertionCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns all insertion costs without any other costs.
- getInsLocal() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getInsLocal() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getInsProb() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getInsSoftDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getJ() - Method in class de.unibi.citec.tcs.alignment.MatrixCoordinate
-
- getJ() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- getJ() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getKey() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- getKeyword(int) - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
-
Returns the keyword for the given index.
- getKeyword() - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
-
Returns the keyword.
- getKeyword() - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractSpecialHTMLTransformer
-
Returns the keyword that serves as column header for the visualization.
- getKeyword() - Method in class de.unibi.citec.tcs.alignment.visualization.PartStringFromFileExternalContent
-
- getKeyword() - Method in interface de.unibi.citec.tcs.alignment.visualization.SpecialHTMLTransformer
-
Returns the keyword that serves as column header for the visualization.
- getKeywordIndex(String) - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
-
Returns the index of the given keyword.
- getKeywords() - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
-
Returns the keywords that are mapped.
- getKeywordSpecification(String) - Method in class de.unibi.citec.tcs.alignment.sequence.NodeSpecification
-
Returns the specification for the given keyword.
- getKeywordSpecification(int) - Method in class de.unibi.citec.tcs.alignment.sequence.NodeSpecification
-
Returns the specification for the given keyword.
- getLastAlignmentMatrix() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
The last matrix that was calculated using this algorithm.
- getLeft() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
-
- getLeft() - Method in class de.unibi.citec.tcs.alignment.Operation
-
- getLeft() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
-
Returns the left input sequence.
- getLength() - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialKeywordSpecification
-
The length all vectors for this keyword have to have.
- getM() - Method in class de.unibi.citec.tcs.alignment.MatrixCoordinate
-
- getMatchScore() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Returns the score used if equal symbols are replaced.
- getMismatchScore() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Returns the score used if different symbols are replaced.
- getNodes() - Method in class de.unibi.citec.tcs.alignment.sequence.Sequence
-
Returns the actual list of nodes.
- getNodeSpecficiation() - Method in class de.unibi.citec.tcs.alignment.sequence.Sequence
-
Returns the NodeSpecification all Nodes in this sequence belong to.
- getNodeSpecification() - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
-
- getNormalizer() - Method in class de.unibi.citec.tcs.alignment.comparators.EuclidianComparator
-
Please refer to the corresponding setter method for more information.
- getNormalizer() - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
-
Please refer to the corresponding setter method for more information.
- getNumberOfParameters() - Method in interface de.unibi.citec.tcs.alignment.comparators.DerivableComparator
-
This shall return the number of parameters of this comparator.
- getNumberOfParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
-
- getNumberOfParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
-
- getNumberOfParameters() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
This shall return the number of parameters of this comparator.
- getNumberOfThreads() - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
-
Please refer to the corresponding setter method for more information.
- getNumberOfThreads() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
Please refer to the corresponding setter method for more information.
- getOperations() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
-
- getOriginalIndex(int) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
-
This is semantically equivalent to
getNodeSpecification().getKeywordIndex(getKeyword(index)) but this is
preprocessed here for better performance.
- getParameterIndex() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- getPath() - Method in class de.unibi.citec.tcs.alignment.Operation
-
- getPathLimit() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
Returns the the number of paths that shall be sampled.
- getPathLimit() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
-
Please refer to the corresponding setter-method for more information.
- getPathLimit() - Method in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
-
Please refer to the corresponding setter method for more calculation.
- getPathMatrix() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
-
This is the dynamic programming matrix calculated by a
SoftAlignmentAlgorithm.
- getPaths(double) - Method in class de.unibi.citec.tcs.alignment.PathMap
-
Returns all paths with the given score.
- getPredecessor() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- getRepCosts() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getReplacementCost(String, String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- getReplacementCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns the whole matrix of replacement costs without gap and skip costs.
- getRepLocal() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getRepLocal() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getRepProb() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getRepSoftDerivative() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getResultClass() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
This method shall return the class of the alignment result.
- getResultClass() - Method in interface de.unibi.citec.tcs.alignment.AlignmentAlgorithm
-
This method shall return the class of the alignment result.
- getResultClass() - Method in interface de.unibi.citec.tcs.alignment.comparators.DerivableComparator
-
Returns the class of the intuitive format of the derivatives for all
parameters of this comparator.
- getResultClass() - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
-
- getResultClass() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
-
- getResultClass() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Returns the class of the intuitive format of the derivatives for all
parameters of this comparator.
- getResultClass() - Method in class de.unibi.citec.tcs.alignment.DynamicTimeWarpingAlgorithm
-
- getResultMatrix() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
This returns the matrix of results if the calculation is done or null if
it has not finished yet.
- getRight() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
-
- getRight() - Method in class de.unibi.citec.tcs.alignment.Operation
-
- getRight() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
-
Returns the right input sequence.
- getScore() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
-
- getScore() - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm.ScoreEntry
-
- getScore() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
-
Returns the soft alignment score between the two input sequences,
normalized between 0 and 1, where 0 means a perfect similarity and 1 a
absolute dissimilarity.
- getScore() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- getScore() - Method in class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm.ScoreEntry
-
- getScore() - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- getScoreMatrix() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
This method will only work if the Result class is Double.
- getScores() - Method in class de.unibi.citec.tcs.alignment.PathMap
-
Get all scores for which paths exist within this map.
- getScoringScheme() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Please refer to the corresponding setter method for more information.
- getSequence() - Method in class de.unibi.citec.tcs.alignment.sequence.Node
-
Returns the sequence this node belongs to.
- getSequences() - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
- getSigma() - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
-
- getSimilarityMatrix() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
-
This is the dynamic programming matrix calculated by a
DynamicTimeWarpingAlgorithm.
- getSimilarityScore() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
-
Returns the softDTW score between the two input sequences.
- getSize() - Method in class de.unibi.citec.tcs.alignment.PathMap
-
Returns the number of paths stored in this map.
- getSkipComparison() - Method in class de.unibi.citec.tcs.alignment.comparators.EuclidianComparator
-
Please refer to the corresponding setter method for more information.
- getSkipComparison() - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
-
Please refer to the corresponding setter method for more information.
- getSkipDeletionCost(String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- getSkipDeletionCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns all skip deletion costs without any other costs.
- getSkipInsertionCost(String) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- getSkipInsertionCosts() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Returns all skip insertion costs without any other costs.
- getSkipScore() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Returns the score used if a symbol is skipped.
- getSkipString() - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
-
The string that is used as reference to determine the
SKIPINSERTION/SKIPDELETION cost of another string.
- getSoftmin() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- getSpecification() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
- getSpecification() - Method in interface de.unibi.citec.tcs.alignment.AlignmentAlgorithm
-
This should return the specification that is used for this Algorithm.
- getSpecification() - Method in class de.unibi.citec.tcs.alignment.DynamicTimeWarpingAlgorithm
-
- getSpecificationClass() - Method in enum de.unibi.citec.tcs.alignment.sequence.ValueType
-
Returns the corresponding specification class for this ValueType.
- getSpecificaton() - Method in class de.unibi.citec.tcs.alignment.AlignmentPath
-
- getSpecificaton() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
-
Returns the AlignmentSpecification that was basis for this Alignment.
- getSpecificaton() - Method in class de.unibi.citec.tcs.alignment.SoftPathModel
-
Returns the AlignmentSpecification that was basis for this Alignment.
- getString() - Method in class de.unibi.citec.tcs.alignment.sequence.StringValue
-
Returns the actual string.
- getSymbol(int) - Method in class de.unibi.citec.tcs.alignment.sequence.Alphabet
-
This is equivalent to "getKeyword"
- getSymbol() - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
-
Returns this actual symbol.
- getSymbolIndex(String) - Method in class de.unibi.citec.tcs.alignment.sequence.Alphabet
-
This is equivalent to "getKeywordIndex"
- getSymbols() - Method in class de.unibi.citec.tcs.alignment.sequence.Alphabet
-
This is equivalent to "getKeywords"
- getType() - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
- getType() - Method in interface de.unibi.citec.tcs.alignment.comparators.Comparator
-
- getType() - Method in class de.unibi.citec.tcs.alignment.comparators.DTWKernelComparator
-
- getType() - Method in class de.unibi.citec.tcs.alignment.comparators.EuclidianComparator
- getType() - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
- getType() - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
- getType() - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
- getType() - Method in class de.unibi.citec.tcs.alignment.Operation
-
- getType() - Method in class de.unibi.citec.tcs.alignment.sequence.AbstractValue
-
Returns the type of this value.
- getType() - Method in class de.unibi.citec.tcs.alignment.sequence.KeywordSpecification
-
Returns the specified type for that keyword.
- getType() - Method in interface de.unibi.citec.tcs.alignment.sequence.Value
-
Returns the type of this value.
- getValue() - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- getValue(String) - Method in class de.unibi.citec.tcs.alignment.sequence.Node
-
Returns the value stored in this Node for the given keyword or null of no
value is stored for the given keyword in this node.
- getValue(int) - Method in class de.unibi.citec.tcs.alignment.sequence.Node
-
Returns the value stored in this Node for the given keyword or null of no
value is stored for the given keyword in this node.
- getValueClass() - Method in enum de.unibi.citec.tcs.alignment.sequence.ValueType
-
The corresponding class of this ValueType.
- getVector() - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
-
Returns the actual vector.
- getWeightedLocalCost() - Method in class de.unibi.citec.tcs.alignment.Operation
-
- getWeighting() - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
-
Returns the current keyword weighting.
- getWeighting() - Method in class de.unibi.citec.tcs.alignment.PathMap
-
Returns the weighting that is used during derivative calculation.
- getWeightThreshold() - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
- getX() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
-
Returns the first input sequence.
- getY() - Method in class de.unibi.citec.tcs.alignment.SoftDTWModel
-
Returns the second input sequence.
- GLOBALAPPROXTHRESHOLD - Static variable in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
This means that softmin arguments with a weight smaller than 10^-3 will
be disregarded.
- GLOBALAPPROXTHRESHOLD - Static variable in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
This means that softmin arguments with a weight smaller than 10^-3 will
be disregarded.
- ScoreBasedWeighting - Enum in de.unibi.citec.tcs.alignment
-
This is a helper class to enable users to weight a collection of scores based
on different schemes specified below.
- Sequence - Class in de.unibi.citec.tcs.alignment.sequence
-
Usually a sequence for alignments is defined as a sequence of symbols.
- Sequence(NodeSpecification) - Constructor for class de.unibi.citec.tcs.alignment.sequence.Sequence
-
Sets up an empty sequence with the given NodeSpecification as basis.
- Sequence(String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.Sequence
-
Sets up a trivial sequence with only one keyword (DEFAULTKEYWORD) and treats
the string content between | delimiters in the input string as symbolic
values.
- Sequence(String, Alphabet) - Constructor for class de.unibi.citec.tcs.alignment.sequence.Sequence
-
Sets up a trivial sequence with only one keyword (DEFAULTKEYWORD) and treats
the string content between | delimiters in the input string as symbolic
values.
- set(int, int, X) - Method in class de.unibi.citec.tcs.alignment.SparseMatrix
-
Sets the value at the given position in the matrix.
- setAlpha(double) - Method in class de.unibi.citec.tcs.alignment.comparators.HyperbolicNormalizer
-
- setApproxThreshold(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
Sets the threshold for which exponents within the softmin function will
be disregarded.
- setApproxThreshold(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
Sets the threshold for which exponents within the softmin function will
be disregarded.
- setBeta(double) - Method in class de.unibi.citec.tcs.alignment.comparators.ExponentialNormalizer
-
- setBeta(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
- setBeta(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
- setBeta(double) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
- setCodeFileContent(Map<String, ArrayList<String>>) - Method in class de.unibi.citec.tcs.alignment.visualization.HTPartStringFromPath
-
Sets codeFileContent, which holds the line-wise content of the
source code files specified by every node.
- setComparator(String, Comparator) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
-
Sets the comparator for a given keyword.
- setComparator(int, Comparator) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
-
Sets the comparator for a given keyword.
- setComparatorDistances(double[]) - Method in class de.unibi.citec.tcs.alignment.Operation
-
Sets the local costs given by the Comparators specified for this
Alignment to align the left Node in this Operation with the right Node
(or deleting, inserting, skipping nodes respectively).
- setCostMatrix(ReplacementCosts) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
-
Sets the ReplacementCosts that shall be used within this Comparator.
- setCostMatrix(double[][]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets the cost matrix itself.
- setDelCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setDeletionCost(String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- setDeletionCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets all deletion costs without any other costs.
- setDelLocal(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setDelProb(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setDelSoftDerivative(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setDoCalculation(boolean[][]) - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
This enables a user to specifically set which pairwise similarity
calculations should be done and which should not be done.
- setFiles(Map<String, File>) - Method in class de.unibi.citec.tcs.alignment.visualization.AbstractHTMLTransformerFromPath
-
Sets the files map directly.
- setGapComparison(double) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclidianComparator
-
If we insert or delete vectors we have no other vector to calculate an
euclidian distance.
- setGapComparison(double) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
-
If we insert or delete vectors we have no other vector to calculate an
L1-norm.
- setGapScore(double) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Specifies the score used if a symbol is deleted or inserted.
- setGapString(String) - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
-
The string that is used as reference to determine the INSERTION/DELETION
cost of another string.
- setInsCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setInsertionCost(String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- setInsertionCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets all insertion costs without any other costs.
- setInsLocal(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setInsProb(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setInsSoftDerivative(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setMatchScore(double) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Specifies the score used if equal symbols are replaced.
- setMismatchScore(double) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Specifies the score used if different symbols are replaced.
- setNormalizer(Normalizer) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclidianComparator
-
The euclidian distance per default is bound by 0 but has no upper bound.
- setNormalizer(Normalizer) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
-
The L1-norm per default is bound by 0 but has no upper bound.
- setNumberOfThreads(int) - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
-
Sets the number of threads that are used.
- setNumberOfThreads(int) - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
Sets the number of threads that are used.
- setPathLimit(int) - Method in class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
This sets the number of paths that shall be sampled.
- setPathLimit(int) - Method in class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
-
The total number of co-optimal alignments can be very huge as multiple
co-optimal operations lead to a combinatorial explosion of possible
alignments.
- setPathLimit(int) - Method in class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
-
This sets the k that gives the StrictKPathAlgorithm its name: The number
of returned AlignmentPaths is limited to the k best alignments.
- setRepCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setReplacementCost(String, String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- setReplacementCosts(double[][]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets the whole matrix of replacement costs without gap and skip costs.
- setRepLocal(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setRepProb(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setRepSoftDerivative(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setScoringScheme(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
This specifies what scoring scheme should be used in this
TrivialEditComparator.
- setSkipComparison(double) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclidianComparator
-
If we skip vectors we have no other vector to calculate an euclidian
distance.
- setSkipComparison(double) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
-
If we skip vectors we have no other vector to calculate an L1-norm.
- setSkipDeletionCost(String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- setSkipDeletionCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets all skip deletion costs without any other costs.
- setSkipInsertionCost(String, double) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- setSkipInsertionCosts(double[]) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
Sets all skip insertion costs without any other costs.
- setSkipScore(double) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
Specifies the score used if a symbol is skipped.
- setSkipString(String) - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
-
The string that is used as reference to determine the
SKIPINSERTION/SKIPDELETION cost of another string.
- setSoftmin(double) - Method in class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- setString(String) - Method in class de.unibi.citec.tcs.alignment.sequence.StringValue
-
- setSymbol(String) - Method in class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
-
Sets the actual symbol.
- setSymmetric(boolean) - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
If this is set to true it is assumed that the desired result of the
alignment is symmetric, meaning that the alignment between the sequences
i and j is equal to the alignment between j and i.
- setUpSpecification(Sequence[]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
-
Sets up a default AlignmentSpecification for the simple
StringEditDistance problem.
- setUpSpecification(Sequence[], double, double, double) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
-
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
- setUpSpecification(Sequence[], double[][]) - Static method in class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
-
Sets up an AlignmentSpecification for the simple
StringEditDistance problem.
- setValue(Double) - Method in class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- setValue(String, Value) - Method in class de.unibi.citec.tcs.alignment.sequence.Node
-
Sets the value for the given keyword.
- setValue(int, Value) - Method in class de.unibi.citec.tcs.alignment.sequence.Node
-
Sets the value for the given keyword.
- setVector(double[]) - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
-
Sets the actual vector.
- setVector(Object) - Method in class de.unibi.citec.tcs.alignment.sequence.VectorialValue
-
Sets the actual vector.
- setVerbose(boolean) - Method in class de.unibi.citec.tcs.alignment.ParallelDerivativeEngine
-
If verbose is set to true the ParallelProcessingEngine will give
information about the current state of the calculation.
- setVerbose(boolean) - Method in class de.unibi.citec.tcs.alignment.ParallelProcessingEngine
-
If verbose is set to true the ParallelProcessingEngine will give
information about the current state of the calculation.
- setWeighting(double[]) - Method in class de.unibi.citec.tcs.alignment.AlignmentSpecification
-
This sets the current weighting of keywords.
- setWeighting(ScoreBasedWeighting) - Method in class de.unibi.citec.tcs.alignment.PathMap
-
Sets the weighting that is used during derivative calculation.
- setWeightThreshold(double) - Method in class de.unibi.citec.tcs.alignment.AbstractGapAlignmentAlgorithm
-
Set a weight threshold (between 0 and 1) that determines which keywords
should be ignored during calculation because their weight is negligible.
- size() - Method in class de.unibi.citec.tcs.alignment.sequence.IndexingScheme
-
Returns the number of mapped keywords.
- SkipComparator<X extends Value> - Interface in de.unibi.citec.tcs.alignment.comparators
-
This further specifies the AlignmentComparator to include skips.
- SKIPDEFAULT - Static variable in class de.unibi.citec.tcs.alignment.comparators.ReplacementCosts
-
- skipDelete(StringValue) - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
-
This should be called during an alignment to retrieve the costs for a
skip deletion of value a from the first sequence.
- skipDelete(VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclidianComparator
-
This should be called during an alignment to retrieve the costs for a
skip deletion of value a from the first sequence.
- skipDelete(VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
-
This should be called during an alignment to retrieve the costs for a
skip deletion of value a from the first sequence.
- skipDelete(SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
-
This should be called during an alignment to retrieve the costs for a
skip deletion of value a from the first sequence.
- skipDelete(X) - Method in interface de.unibi.citec.tcs.alignment.comparators.SkipComparator
-
This should be called during an alignment to retrieve the costs for a
skip deletion of value a from the first sequence.
- skipDelete(SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
This should be called during an alignment to retrieve the costs for a
skip deletion of value a from the first sequence.
- skipInsert(StringValue) - Method in class de.unibi.citec.tcs.alignment.comparators.CharStatComparator
-
This should be called during an alignment to retrieve the costs for a
skip insertion of value b into the first sequence.
- skipInsert(VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.EuclidianComparator
-
This should be called during an alignment to retrieve the costs for a
skip insertion of value b into the first sequence.
- skipInsert(VectorialValue) - Method in class de.unibi.citec.tcs.alignment.comparators.L1NormComparator
-
This should be called during an alignment to retrieve the costs for a
skip insertion of value b into the first sequence.
- skipInsert(SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.ReplacementComparator
-
This should be called during an alignment to retrieve the costs for a
skip insertion of value b into the first sequence.
- skipInsert(X) - Method in interface de.unibi.citec.tcs.alignment.comparators.SkipComparator
-
This should be called during an alignment to retrieve the costs for a
skip insertion of value b into the first sequence.
- skipInsert(SymbolicValue) - Method in class de.unibi.citec.tcs.alignment.comparators.TrivialEditComparator
-
This should be called during an alignment to retrieve the costs for a
skip insertion of value b into the first sequence.
- SoftAlignmentFullAlgorithm - Class in de.unibi.citec.tcs.alignment
-
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
- SoftAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.SoftAlignmentFullAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- SoftAlignmentSamplingAlgorithm - Class in de.unibi.citec.tcs.alignment
-
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
- SoftAlignmentSamplingAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.SoftAlignmentSamplingAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- SoftAlignmentScoreAlgorithm - Class in de.unibi.citec.tcs.alignment
-
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
- SoftAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- SoftAlignmentScoreAlgorithm.ScoreEntry - Class in de.unibi.citec.tcs.alignment
-
- SoftAlignmentScoreAlgorithm.ScoreEntry(double) - Constructor for class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm.ScoreEntry
-
- SoftDTWModel - Class in de.unibi.citec.tcs.alignment
-
storage unit for soft DTW alignment result, provides functions to calculate
the soft DTW derivatives based on the stored soft alignment
- SoftDTWModel(AlignmentSpecification, Sequence, Sequence, double[][]) - Constructor for class de.unibi.citec.tcs.alignment.SoftDTWModel
-
- softmin(double, double...) - Static method in class de.unibi.citec.tcs.alignment.SoftAlignmentScoreAlgorithm
-
This calculates softmin for the given input and the given value of beta.
- SoftPathModel - Class in de.unibi.citec.tcs.alignment
-
This is the soft pendant to the AlignmentPath.
- SoftPathModel(AlignmentSpecification, Sequence, Sequence, double, double, SoftPathModel.SoftMatrixEntry[][]) - Constructor for class de.unibi.citec.tcs.alignment.SoftPathModel
-
- SoftPathModel.SoftMatrixEntry - Class in de.unibi.citec.tcs.alignment
-
- SoftPathModel.SoftMatrixEntry() - Constructor for class de.unibi.citec.tcs.alignment.SoftPathModel.SoftMatrixEntry
-
- SOURCE_CODE_FILE_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
-
- SOURCE_CODE_PART_KEYWORD - Static variable in class de.unibi.citec.tcs.alignment.visualization.Keywords
-
- SparseDerivableComparator<X extends Value,Y> - Interface in de.unibi.citec.tcs.alignment.comparators
-
Some derivable comparators have the special property that in each alignment
step only a small subset of parameters is needed.
- SparseLocalDerivative - Interface in de.unibi.citec.tcs.alignment.comparators
-
This is an interface for classes that are able to hold sparse representations
of a local derivative, where only for one or a few parameters the derivative
is non-zero.
- SparseLocalDerivative.FixedSparseLocalDerivative - Class in de.unibi.citec.tcs.alignment.comparators
-
This implements the SparseLocalDerivative interface for a fixed number of
entries.
- SparseLocalDerivative.FixedSparseLocalDerivative(int) - Constructor for class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FixedSparseLocalDerivative
-
- SparseLocalDerivative.FlexibleSparseLocalDerivative - Class in de.unibi.citec.tcs.alignment.comparators
-
- SparseLocalDerivative.FlexibleSparseLocalDerivative() - Constructor for class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.FlexibleSparseLocalDerivative
-
- SparseLocalDerivative.SparseDeriativeEntry - Class in de.unibi.citec.tcs.alignment.comparators
-
- SparseLocalDerivative.SparseDeriativeEntry(int, double) - Constructor for class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.SparseDeriativeEntry
-
- SparseLocalDerivative.TrivialSparseLocalDerivative - Class in de.unibi.citec.tcs.alignment.comparators
-
This is a representation with just one entry.
- SparseLocalDerivative.TrivialSparseLocalDerivative() - Constructor for class de.unibi.citec.tcs.alignment.comparators.SparseLocalDerivative.TrivialSparseLocalDerivative
-
- SparseMatrix<X> - Class in de.unibi.citec.tcs.alignment
-
This models a sparse matrix that does not have to be fully calculated.
- SparseMatrix() - Constructor for class de.unibi.citec.tcs.alignment.SparseMatrix
-
- SpecialHTMLTransformer - Interface in de.unibi.citec.tcs.alignment.visualization
-
Interface to transform some sequence into HTML code.
- StrictAlignmentFullAlgorithm - Class in de.unibi.citec.tcs.alignment
-
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
- StrictAlignmentFullAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- StrictAlignmentFullAlgorithm.FullMatrixEntry - Class in de.unibi.citec.tcs.alignment
-
- StrictAlignmentFullAlgorithm.FullMatrixEntry(double, int, int, StrictAlignmentFullAlgorithm.FullMatrixEntry) - Constructor for class de.unibi.citec.tcs.alignment.StrictAlignmentFullAlgorithm.FullMatrixEntry
-
- StrictAlignmentScoreAlgorithm - Class in de.unibi.citec.tcs.alignment
-
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
- StrictAlignmentScoreAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- StrictAlignmentScoreAlgorithm.ScoreEntry - Class in de.unibi.citec.tcs.alignment
-
- StrictAlignmentScoreAlgorithm.ScoreEntry(double) - Constructor for class de.unibi.citec.tcs.alignment.StrictAlignmentScoreAlgorithm.ScoreEntry
-
- StrictAllOptimalAlgorithm - Class in de.unibi.citec.tcs.alignment
-
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
- StrictAllOptimalAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- StrictAllOptimalAlgorithm.FullMatrixEntry - Class in de.unibi.citec.tcs.alignment
-
- StrictAllOptimalAlgorithm.FullMatrixEntry(double, double, double, double, int, int) - Constructor for class de.unibi.citec.tcs.alignment.StrictAllOptimalAlgorithm.FullMatrixEntry
-
- StrictKPathAlgorithm - Class in de.unibi.citec.tcs.alignment
-
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
- StrictKPathAlgorithm(AlignmentSpecification) - Constructor for class de.unibi.citec.tcs.alignment.StrictKPathAlgorithm
-
This sets up an AlignmentAlgorithm instance according to the given
specification.
- StringEditDistance - Class in de.unibi.citec.tcs.alignment.wrappers
-
This is a simple wrapper to support an easier interface for the simple
StringEditDistance problem.
- StringEditDistance() - Constructor for class de.unibi.citec.tcs.alignment.wrappers.StringEditDistance
-
- StringKeywordSpecification - Class in de.unibi.citec.tcs.alignment.sequence
-
This specifies String keywords which are not especially restricted.
- StringKeywordSpecification(String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.StringKeywordSpecification
-
- StringValue - Class in de.unibi.citec.tcs.alignment.sequence
-
This value is supposed to represent strings that are not restricted to a
certain alphabet.
- StringValue() - Constructor for class de.unibi.citec.tcs.alignment.sequence.StringValue
-
- StringValue(String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.StringValue
-
- SymbolicKeywordSpecification - Class in de.unibi.citec.tcs.alignment.sequence
-
This specifies symbolic keywords by their alphabet.
- SymbolicKeywordSpecification(Alphabet, String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.SymbolicKeywordSpecification
-
- SymbolicValue - Class in de.unibi.citec.tcs.alignment.sequence
-
This is a special value class that is restricted to a finite list of values
defined by an alphabet.
- SymbolicValue(Alphabet) - Constructor for class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
-
- SymbolicValue(Alphabet, String) - Constructor for class de.unibi.citec.tcs.alignment.sequence.SymbolicValue
-