org.appliedtopology.tda4j
Package for the Scala library TDA4j
Attributes
Members list
Type members
Experimental classlikes
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class HelixDelaunayclass MiniballDelaunay
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trait Serializabletrait Producttrait Equalstrait SpatialQuery[VertexT]class Objecttrait Matchableclass AnyShow all
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trait OrderedCell
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trait IterableOnce[CellT]trait Filterable[FiltrationT]class Objecttrait Matchableclass AnyShow all
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class MaskedSymmetricRipserStream[KeyT]class RipserStreamBaseclass RipserStreamclass SymmetricRipserStream[KeyT]class RipserStreamOf[VertexT]class RipserStreamSparseclass AlphaShapesclass HelixDelaunayclass MiniballDelaunayShow all
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class Objecttrait Matchableclass Any
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class Objecttrait Matchableclass Any
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trait OrderedCocell
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******* Optimized Vietoris-Rips cofacet generation for fast coboundary computation *******
******* Optimized Vietoris-Rips cofacet generation for fast coboundary computation *******
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trait Serializabletrait Producttrait Equalstrait Iterator[VertexT]trait IterableOnceOps[VertexT, Iterator, Iterator[VertexT]]trait IterableOnce[VertexT]class Objecttrait Matchableclass AnyShow all
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trait Serializabletrait Producttrait Equalsclass Objecttrait Matchableclass AnyShow all
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trait Serializabletrait Producttrait Equalsclass Objecttrait Matchableclass AnyShow all
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class Objecttrait Matchableclass Any
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EuclideanMetricSpace.type
Takes in an point cloud and computes the Euclidean distance on demand.
Takes in an point cloud and computes the Euclidean distance on demand.
Value parameters
- pts
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Point cloud matrix represented as a
Seq[Seq[Double]]. The class expects but does not enforce:pts(x1).size == pts(x2).sizefor allx1,x2
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A symmetry-aware compressed indexed sequence container that keeps track of representatives of each orbit, and generates the rest of the orbit as and when needed, including an iterator structure that also only generates the rest of the orbit when needed, and a method for checking whether a particular simplex is an orbit representatives in a way that does not hold on to orbit elements (thus allowing them to get instantly garbage collected).
A symmetry-aware compressed indexed sequence container that keeps track of representatives of each orbit, and generates the rest of the orbit as and when needed, including an iterator structure that also only generates the rest of the orbit when needed, and a method for checking whether a particular simplex is an orbit representatives in a way that does not hold on to orbit elements (thus allowing them to get instantly garbage collected).
Type parameters
- KeyT
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The type of the group element indices.
- VertexT
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The type of the vertices.
Value parameters
- ordering$VertexT$0
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We depend on a total order of simplices, which we generate from a total order of vertices. This carries that ordering.
- representatives
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A sequence of simplices, each representative for its own orbit
- symmetry
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A
SymmetryGroupobject carrying information about symmetries
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trait Puretrait Equalsclass Objecttrait Matchableclass AnyShow all
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Takes in an explicit distance matrix, and performs lookups in this distance matrix.
Takes in an explicit distance matrix, and performs lookups in this distance matrix.
Value parameters
- dist
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Distance matrix represented as a
Seq[Seq[Double]]. The class expects but does not enforce:dist(x1).size == dist(x2).sizefor allx1,x2dist(x).size == dist.sizefor allxdist(x)(x) == 0for allx- The triangle inequality
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trait Clearableclass Objecttrait Matchableclass AnyShow all
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class Objecttrait Matchableclass Any
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class Objecttrait Matchableclass Any
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class MaskedSymmetricRipserStream[KeyT]class RipserStreamBaseclass RipserStreamclass SymmetricRipserStream[KeyT]class RipserStreamOf[VertexT]class RipserStreamSparseclass AlphaShapesclass HelixDelaunayclass MiniballDelaunaytrait DoubleFiltration[CellT]Show all
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class MaskedSymmetricRipserStream[KeyT]class RipserStreamBaseclass RipserStreamclass SymmetricRipserStream[KeyT]class RipserStreamOf[VertexT]class RipserStreamSparseclass AlphaShapesclass HelixDelaunayclass MiniballDelaunaytrait DoubleFiltration[CellT]Show all
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class Objecttrait Matchableclass Any
Convenience functionality for metric spaces.
Convenience functionality for metric spaces.
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class Objecttrait Matchableclass Any
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FiniteMetricSpace.type
Interface for being a finite metric space
Interface for being a finite metric space
Type parameters
- VertexT
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Type of the vertex indices for the metric space
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class Objecttrait Matchableclass Any
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class EuclideanMetricSpaceclass ExplicitMetricSpaceclass HyperCubeclass HyperCubeBitSetclass IntMetricSpace[VertexT]class SparseMetricSpace[VertexT]Show all
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trait Sumtrait Mirrorclass Objecttrait Matchableclass Any
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FractionalExpr.type
This functionality is an experiment in using algebraic effect structures for flexible coefficient choices. The idea is that each actual computation that is needed is built up as an AST, and simplified; and a coefficient choice is an effect handler that evaluates the remainder in the field of coefficients to be used.
This functionality is an experiment in using algebraic effect structures for flexible coefficient choices. The idea is that each actual computation that is needed is built up as an AST, and simplified; and a coefficient choice is an effect handler that evaluates the remainder in the field of coefficients to be used.
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class Objecttrait Matchableclass Any
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object doubleHandler
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class Objecttrait Matchableclass Any
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Based on https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10917453&tag=1
Value parameters
- pts
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- the input points to triangulate
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Attributes
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The HyperCube example of a symmetric point set. Vertices are all binary strings of length bitlength. Distances on the hypercube are Hamming distances between binary strings, ie how many bits differ between the two strings.
The HyperCube example of a symmetric point set. Vertices are all binary strings of length bitlength. Distances on the hypercube are Hamming distances between binary strings, ie how many bits differ between the two strings.
Binary strings are throughout represented as immutable.BitSet.
Value parameters
- bitlength
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The dimension of the hypercube.
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Symmetry group of the hypercube under permutations of bit positions. No rotations of the hypercube included here.
Symmetry group of the hypercube under permutations of bit positions. No rotations of the hypercube included here.
Value parameters
- bitlength
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Dimension of the hypercube.
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trait Producttrait Mirrorclass Objecttrait Matchableclass Any
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Hyperplane.type
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trait Serializabletrait Producttrait Equalsclass Objecttrait Matchableclass AnyShow all
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trait Serializabletrait Producttrait Equalsclass Objecttrait Matchableclass AnyShow all
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class Objecttrait Matchableclass Any
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Hypersphere.type
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Wrapper class to make any metricspace into a metricspace defined on indices 0 through metricSpace.size. This way, code can assume that the index set is contiguous.
Wrapper class to make any metricspace into a metricspace defined on indices 0 through metricSpace.size. This way, code can assume that the index set is contiguous.
Type parameters
- VertexT
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Type of the vertex indices for the wrapped metric space
Value parameters
- metricSpace
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Wrapped metric space
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trait Serializabletrait Producttrait Equalstrait SpatialQuery[VertexT]class Objecttrait Matchableclass AnyShow all
This implementation of Kruskal's algorithm will return two iterators of vertex pairs: the first iterator is a Minimal Spanning Tree in increasing weight order, while the second iterator gives all the non-included
This implementation of Kruskal's algorithm will return two iterators of vertex pairs: the first iterator is a Minimal Spanning Tree in increasing weight order, while the second iterator gives all the non-included
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class Objecttrait Matchableclass Any
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class Objecttrait Matchableclass Any
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Trait that defines what it means to have an ordered basis
Trait that defines what it means to have an ordered basis
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class Objecttrait Matchableclass Any
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This class enumerates permutations in order to allow permutations of bit-positions to fill out the symmetry group of the hypercube.
This class enumerates permutations in order to allow permutations of bit-positions to fill out the symmetry group of the hypercube.
Value parameters
- elementCount
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How many objects are permuted?
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class Objecttrait Matchableclass Any
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class Objecttrait Matchableclass Any
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class Objecttrait Matchableclass Any
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Point.type
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trait Serializabletrait Producttrait Equalsclass Objecttrait Matchableclass AnyShow all
Specifies what it means for the type Self to be a module (or vector space) over the [Numeric] (ie ring-like) type R.
Specifies what it means for the type Self to be a module (or vector space) over the [Numeric] (ie ring-like) type R.
A minimal implementation of this trait will define zero, plus, scale, and at least one of minus and negate
Type parameters
- R
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Type of the ring coefficients
- Self
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Type of the module elements.
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class Objecttrait Matchableclass Any
****** Maybe @deprecate or outright everything below here? ******
****** Maybe @deprecate or outright everything below here? ******
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class Objecttrait Matchableclass Any
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class SymmetricRipserStream[KeyT]
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class Objecttrait Matchableclass Any
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RipserStream.type
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class RipserStreamclass SymmetricRipserStream[KeyT]
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trait PointSetclass Objecttrait Matchableclass Any
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class Objecttrait Matchableclass Any
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Simplex.type
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trait Producttrait Mirrorclass Objecttrait Matchableclass Any
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SimplexEdge.type
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trait Serializabletrait Producttrait Equalsclass Objecttrait Matchableclass AnyShow all
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class Objecttrait Matchableclass Any
Abstract trait for representing a sequence of simplices.
Abstract trait for representing a sequence of simplices.
Type parameters
- FiltrationT
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Type of the filtration values.
- VertexT
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Type of vertices of the contained simplices.
Attributes
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We may want to change this to inherit instead from
IterableOnce[Simplex[VertexT]], so that a lazy computed simplex stream can be created and fit in the type hierarchy. - Companion
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class MaskedSymmetricRipserStream[KeyT]class RipserStreamBaseclass RipserStreamclass SymmetricRipserStream[KeyT]class RipserStreamOf[VertexT]class RipserStreamSparseShow all
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class Objecttrait Matchableclass Any
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SimplexStream.type
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class Objecttrait Matchableclass Any
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class Objecttrait Matchableclass Any
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****** Sparse Metric Spaces and the Dory storage *******
****** Sparse Metric Spaces and the Dory storage *******
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trait Serializabletrait Producttrait Equalstrait FiniteMetricSpace[VertexT]class Objecttrait Matchableclass AnyShow all
******* Efficient Spatial Queries *******
******* Efficient Spatial Queries *******
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class Objecttrait Matchableclass Any
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class BruteForce[VertexT]class JVPTree[VertexT]
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trait IterableOnce[CellT]trait Filterable[FiltrationT]class Objecttrait Matchableclass AnyShow all
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class Objecttrait Matchableclass Any
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class RipserStreamclass RipserStreamBasetrait Filterable[Double]class Objecttrait Matchableclass AnyShow all
Symmetry-aware version of Zomorodian's incremental algorithm for generating Vietoris-Rips complexes. The algorithm object needs access to a SymmetryGroup instance that encodes all we know about the symmetries.
Symmetry-aware version of Zomorodian's incremental algorithm for generating Vietoris-Rips complexes. The algorithm object needs access to a SymmetryGroup instance that encodes all we know about the symmetries.
Type parameters
- KeyT
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Type of the indices for the group elements in
symmetry. - VertexT
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Type of the vertices of the complex.
Value parameters
- ordering$VertexT$0
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We need to sort simplices, so we need to sort vertices.
- symmetry
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Symmetry group details.
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class Objecttrait Matchableclass Any
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A trait encoding the interface for a group of symmetries acting on the vertex set of a simplicial complex. The group and its action needs to be fully known and implemented.
A trait encoding the interface for a group of symmetries acting on the vertex set of a simplicial complex. The group and its action needs to be fully known and implemented.
This structure assumes that you can provide a group action on vertices, and will from that deduce a group action on simplices by acting pointwise: g.[a,b,c] = [ga,gb,gc], collapsing any degeneracies.
A fundamentally important part of the symmetry group action for our applications is to be able to pick out canonical representatives for each orbit, and to recognize when a simplex is such a canonical representative.
Type parameters
- KeyT
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The type used to enumerate the group elements.
- VertexT
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The type of the vertices.
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class Objecttrait Matchableclass Any
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class HyperCubeSymmetryclass HyperCubeSymmetryBitSet
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class Objecttrait Matchableclass Any
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trait Serializabletrait Producttrait Equalsclass Objecttrait Matchableclass AnyShow all
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class Objecttrait Matchableclass Any
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doubleHandler.type
Types
Simplices really are just sets, outright. We provide an implementation of the [OrderedCell] typeclass for simplicial complex structures, to enable their use.
Simplices really are just sets, outright. We provide an implementation of the [OrderedCell] typeclass for simplicial complex structures, to enable their use.
Attributes
Value members
Experimental methods
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Givens
Experimental givens
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A given instance that allows us to automatically sort bitsets lexicographically.
A given instance that allows us to automatically sort bitsets lexicographically.
Attributes
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Extensions
Experimental extensions
Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
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- true
Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
- Experimental
- true
Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
- Experimental
- true
Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
- Experimental
- true
Inherit a selection of the SortedSet methods and add other utility methods
Inherit a selection of the SortedSet methods and add other utility methods
Attributes
- Experimental
- true