Index

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _

A

absApproximation(double, double) - Static method in class edu.stanford.math.plex4.utility.MathUtility
AbstractFilteredStream<T> - Interface in edu.stanford.math.plex4.streams.interfaces: This interface defines the functionality of a streamed filtered chain complex.
AbstractHomologyTracker<K,I extends java.lang.Comparable,U,G> - Interface in edu.stanford.math.plex4.homology.zigzag
AbstractIntMetricSpace - Interface in edu.stanford.math.plex4.metric.interfaces: This interface defines the functionality of a finite metric space where the objects are indexed by integers.
AbstractMultifilteredStream<T> - Interface in edu.stanford.math.plex4.streams.multi
AbstractObjectMetric<T> - Interface in edu.stanford.math.plex4.metric.interfaces: This interface defines a metric on the type T.
AbstractObjectMetricSpace<T> - Interface in edu.stanford.math.plex4.metric.interfaces: This interface defines the functionality of a finite metric space whose points are of type T.
AbstractPersistenceAlgorithm<T> - Class in edu.stanford.math.plex4.homology.interfaces: This interface defines the functionality of a persistence algorithm.
AbstractPersistenceAlgorithm() - Constructor for class edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceAlgorithm
AbstractPersistenceBasisAlgorithm<T,B> - Class in edu.stanford.math.plex4.homology.interfaces: This interface defines the functionality of a persistence algorithm that also produces generators for each calculated interval.
AbstractPersistenceBasisAlgorithm() - Constructor for class edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceBasisAlgorithm
AbstractPersistenceTracker<K,I extends java.lang.Comparable,G> - Interface in edu.stanford.math.plex4.homology.zigzag
AbstractSearchableMetricSpace<T> - Interface in edu.stanford.math.plex4.metric.interfaces: This interface defines the functionality of a metric space with various querying capabilities.
AbstractStreamFlattener<T> - Interface in edu.stanford.math.plex4.streams.multi
AbstractUndirectedGraph - Interface in edu.stanford.math.plex4.graph: This interface abstracts the functionality of an unweighted graph.
AbstractVisualizer - Class in edu.stanford.math.plex4.visualization: Abstract class for visualizing a 3D point cloud and the persistent homology classes corresponding to the Vietoris Rips filtration.
AbstractVisualizer() - Constructor for class edu.stanford.math.plex4.visualization.AbstractVisualizer
AbstractWeightedUndirectedGraph - Interface in edu.stanford.math.plex4.graph: This interface defines functionality for a weighted graph.
actionPerformed(ActionEvent) - Method in class edu.stanford.math.plex.BCPlot.fileSaveMenuHandler: Action events handler
add(Chain, int) - Method in class edu.stanford.math.plex.Chain: Add one chain to another.
add(Simplex, double) - Method in class edu.stanford.math.plex.ExplicitStream
add(int[], double) - Method in class edu.stanford.math.plex.ExplicitStream: Add a simplex, specified by its vertex vector and persistence parameter, to the stream.
add(double[], double) - Method in class edu.stanford.math.plex.ExplicitStream: Add a simplex, specified by its vertex vector and persistence parameter, to the stream.
add(int[][], double[]) - Method in class edu.stanford.math.plex.ExplicitStream: Add an array of simplices, specified by matching vertex vectors and persistence parameters, to the stream.
add(double[][], double[]) - Method in class edu.stanford.math.plex.ExplicitStream: Add an array of simplices, specified by matching vertex vectors and persistence parameters, to the stream.
add(U, K) - Method in interface edu.stanford.math.plex4.homology.zigzag.AbstractHomologyTracker
add(U) - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
add(U, int) - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
add(U, Integer) - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
add(U, Integer) - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
addAllElements(AbstractFilteredStream<T>) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitStream: This function copies all of the elements in the supplied stream to the current one.
addCofaces(UndirectedWeightedListGraph, int, Simplex, TIntHashSet, double) - Method in class edu.stanford.math.plex4.streams.impl.FlagComplexStream: This function inductively adds all of the cofaces of the simplex tau to the complex.
addColumn(String) - Method in class edu.stanford.math.plex4.io.Table: This function adds a new column to the table.
addEdge(int, int, int) - Method in class edu.stanford.math.plex4.bottleneck.FlowNetwork
addEdge(int, int, double) - Method in class edu.stanford.math.plex4.bottleneck.WeightedBipartiteGraph
addEdge(int, int) - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph: This function adds the edge (i, j) to the graph.
addEdge(int, int, double) - Method in interface edu.stanford.math.plex4.graph.AbstractWeightedUndirectedGraph: This function adds an edge with specified weight.
addEdge(int, int) - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph
addEdge(int, int, double) - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
addEdge(int, int) - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
addElement(Cell, double) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitCellStream
addElement(int[]) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream: This function adds a simplex with the provided vertices.
addElement(int[], double) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream: This function adds a simplex with the provided vertices and given filtration index.
addElement(T, double) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitStream: This function adds a basis element the stream with specified filtration index.
addElement(T, double[]) - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
addElement(T, int) - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
addElement(T, int) - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
addElement(T, int) - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function adds the given basis element to the storage structure, with the supplied filtration index.
addInterval(int, T, T, G) - Method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection: This function adds the specified finite interval (start, end} at the supplied dimension.
addInterval(int, T, T) - Method in class edu.stanford.math.plex4.homology.barcodes.BarcodeCollection: This function adds the specified finite interval (start, end} at the supplied dimension.
addInterval(int, Interval<T>) - Method in class edu.stanford.math.plex4.homology.barcodes.BarcodeCollection
addInterval(int, I, G) - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function adds an interval and generator at the specified dimension to the collection.
addLeftInfiniteInterval(int, T, G) - Method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection: This function adds the specified semi-infinite interval {-infinity, end} at the supplied dimension.
addLeftInfiniteInterval(int, T) - Method in class edu.stanford.math.plex4.homology.barcodes.BarcodeCollection: This function adds the specified semi-infinite interval {-infinity, end} at the supplied dimension.
addNewVertex() - Method in class edu.stanford.math.plex4.streams.impl.ExplicitCellStream: This adds a new vertex to the cell complex.
addRightInfiniteInterval(int, T, G) - Method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection: This function adds the specified semi-infinite interval {start, infinity} at the supplied dimension.
addRightInfiniteInterval(int, T) - Method in class edu.stanford.math.plex4.homology.barcodes.BarcodeCollection: This function adds the specified semi-infinite interval {start, infinity} at the supplied dimension.
addRow(Collection<Object>) - Method in class edu.stanford.math.plex4.io.Table: This function adds a data row to the table.
addRow(List<String>) - Method in class edu.stanford.math.plex4.io.Table: This function adds a data row to the table.
addRow(String[], boolean) - Method in class edu.stanford.math.plex4.io.Table: This function adds a data row to the table.
addVertex(int) - Method in class edu.stanford.math.plex.Simplex: Add a vertex to a simplex.
addVertex(int, int) - Method in class edu.stanford.math.plex.Simplex: Add a vertex to a simplex, and set the findex.
addVertex(int) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream: This function adds a new vertex to the complex with a filtration index of 0.
addVertex(int, double) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream: This function adds a new vertex to the complex with specified filtration index.
alexanderWhitneyDiagonal(Simplex) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function computes the Alexander-Whitney diagonal map of a given simplex defined by Delta([v_0, ...
alternatingCoefficients(int, int) - Static method in class edu.stanford.math.plex.Chain
AnnotatedBarcodeCollection<T extends java.lang.Comparable<T>,G> - Class in edu.stanford.math.plex4.homology.barcodes
AnnotatedBarcodeCollection() - Constructor for class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection
annotatedBarcodes - Variable in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
appendColumn(Map<Integer, X>, X) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
appendToArray(int[], int) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility: This function appends the argument newValue to the end of the supplied array.
ArrayUtility - Class in edu.stanford.math.plex4.utility
ArrayUtility() - Constructor for class edu.stanford.math.plex4.utility.ArrayUtility
assert_2_vertices(int[]) - Static method in class edu.stanford.math.plex.Packed2Simplex
assert_4_vertices(int[]) - Static method in class edu.stanford.math.plex.Packed4Simplex
assert_6_vertices(int[]) - Static method in class edu.stanford.math.plex.Packed6Simplex
assert_8_vertices(int[]) - Static method in class edu.stanford.math.plex.Packed8Simplex
assignValue(String, double) - Method in class edu.stanford.math.plex4.io.MatlabWriter
assignValue(String, int) - Method in class edu.stanford.math.plex4.io.MatlabWriter
attachNewCell(int, int[]) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitCellStream: This adds a new cell to the complex with boundary specified by the supplied array of cell ids.
attachNewCell(int, int[], int[]) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitCellStream: This adds a new cell to the complex with boundary and boundary coefficients given.
attachNewCellToPoint(int, int) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitCellStream: This attaches a n-cell to an existing point in the complex.

B

B - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
backgroundImageName - Variable in class edu.stanford.math.plex.BCPlot
backwardBurningProbability - Variable in class edu.stanford.math.plex4.graph.random.ForestFireGraph
BAGraph - Class in edu.stanford.math.plex4.graph.random: Implements a Barabasi-Albert (BA) random graph model.
BAGraph(int, int) - Constructor for class edu.stanford.math.plex4.graph.random.BAGraph
barcodeBarColor - Variable in class edu.stanford.math.plex.BCPlot
barcodeBarHeight - Variable in class edu.stanford.math.plex.BCPlot
barcodeBarSpacing - Variable in class edu.stanford.math.plex.BCPlot
BarcodeCollection<T extends java.lang.Comparable<T>> - Class in edu.stanford.math.plex4.homology.barcodes
BarcodeCollection() - Constructor for class edu.stanford.math.plex4.homology.barcodes.BarcodeCollection
barcodePane - Variable in class edu.stanford.math.plex.BCPlot
BarcodeUtility - Class in edu.stanford.math.plex4.homology.barcodes
BarcodeUtility() - Constructor for class edu.stanford.math.plex4.homology.barcodes.BarcodeUtility
BarcodeVisualizer - Class in edu.stanford.math.plex4.visualization: This class contains functions for visualizing barcodes.
BarcodeVisualizer() - Constructor for class edu.stanford.math.plex4.visualization.BarcodeVisualizer
BarcodeVisualizer.BarAppearance - Class in edu.stanford.math.plex4.visualization
BarcodeVisualizer.BarAppearance(int, int) - Constructor for class edu.stanford.math.plex4.visualization.BarcodeVisualizer.BarAppearance
BarcodeWriter - Class in edu.stanford.math.plex4.io
baseModulus() - Static method in class edu.stanford.math.plex.Persistence: What is modulus of the coefficient field?
baseModulus() - Static method in class edu.stanford.math.plex.PersistenceBasis: What is modulus of the coefficient field?
baseRegionUsedForPlotLegendRulerLabels - Variable in class edu.stanford.math.plex.BCPlot
basis(SimplexStream, int, double) - Static method in class edu.stanford.math.plex.PersistenceBasis
basis() - Method in class edu.stanford.math.plex.PersistenceBasisInterval: The basis representing the interval.
basis() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Float: Retrieves the basis element of an interval.
basis() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Int: Retrieves the basis element of an interval.
basisComparator - Variable in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This comparator defines the ordering on the basis elements.
basisComparator - Variable in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This comparator defines the ordering on the basis elements.
basisComparator - Variable in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This comparator defines the ordering on the basis elements.
basisComparator - Variable in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This comparator defines the ordering on the basis elements.
basisComparator - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
basisComparator - Variable in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker: This comparator defines the ordering on the basis elements.
basisComparator - Variable in class edu.stanford.math.plex4.homology.zigzag.ZigZagHomology: This comparator defines the ordering on the basis elements.
basisElement - Variable in class edu.stanford.math.plex.PersistenceBasisInterval.Float
basisElement - Variable in class edu.stanford.math.plex.PersistenceBasisInterval.Int
basisElements - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
BasisTrackingUtility - Class in edu.stanford.math.plex4.homology.zigzag: This class contains various static functions for assisting with zigzag homology computations.
BasisTrackingUtility() - Constructor for class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
BCPlot - Class in edu.stanford.math.plex: The BCPlot class does simple plotting of PersistenceIntervals.
BCPlot() - Constructor for class edu.stanford.math.plex.BCPlot
BCPlot(double[][], double, boolean) - Constructor for class edu.stanford.math.plex.BCPlot
BCPlot.DrawingPane - Class in edu.stanford.math.plex: The component inside the scroll pane.
BCPlot.DrawingPane() - Constructor for class edu.stanford.math.plex.BCPlot.DrawingPane
BCPlot.fileSaveMenuHandler - Class in edu.stanford.math.plex
BCPlot.fileSaveMenuHandler(String, ImageIcon, String, Integer) - Constructor for class edu.stanford.math.plex.BCPlot.fileSaveMenuHandler
BCPlot.Ruler - Class in edu.stanford.math.plex
BCPlot.Ruler(BCPlot.DrawingPane) - Constructor for class edu.stanford.math.plex.BCPlot.Ruler
BifilteredMetricStream<T extends PrimitiveBasisElement> - Class in edu.stanford.math.plex4.streams.multi
BifilteredMetricStream(PrimitiveStream<T>, FilterFunction<T>) - Constructor for class edu.stanford.math.plex4.streams.multi.BifilteredMetricStream
BinaryHierarchicalGraph - Class in edu.stanford.math.plex4.graph.random: Makes a random hierarchical graph by considering points P = {1,2,...,n} and partitions C_{i,j}, where j is the granularity.
BinaryHierarchicalGraph(int) - Constructor for class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
BinaryHierarchicalGraph(int, double) - Constructor for class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
BinaryHierarchicalGraph(int, boolean) - Constructor for class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph: Creates a HierarchicalGraph without any edges.
BinaryTree - Class in edu.stanford.math.plex4.graph.random: Implements a binary tree of nodes labeled 1,2,...,n.
BinaryTree(int) - Constructor for class edu.stanford.math.plex4.graph.random.BinaryTree
BinaryTreeGraph - Class in edu.stanford.math.plex4.graph.random
BinaryTreeGraph(int) - Constructor for class edu.stanford.math.plex4.graph.random.BinaryTreeGraph
bins - Variable in class edu.stanford.math.mapper.HistogramCreator
bits - Variable in class edu.stanford.math.plex.Packed2Simplex
bits_hi - Variable in class edu.stanford.math.plex.Packed4Simplex
bits_hi - Variable in class edu.stanford.math.plex.Packed6Simplex
bits_hi - Variable in class edu.stanford.math.plex.Packed8Simplex
bits_hi_mid - Variable in class edu.stanford.math.plex.Packed8Simplex
bits_lo - Variable in class edu.stanford.math.plex.Packed4Simplex
bits_lo - Variable in class edu.stanford.math.plex.Packed6Simplex
bits_lo - Variable in class edu.stanford.math.plex.Packed8Simplex
bits_lo_mid - Variable in class edu.stanford.math.plex.Packed8Simplex
bits_mid - Variable in class edu.stanford.math.plex.Packed6Simplex
BooleanAbsoluteHomology - Class in edu.stanford.math.plex4.autogen.homology
BooleanAbsoluteHomology(Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.BooleanAbsoluteHomology: This constructor initializes the object with a comparator on the basis type.
BooleanClassicalHomology - Class in edu.stanford.math.plex4.autogen.homology: This class performs the persistent homology algorithm as outlined in the paper "Computing Persistent Homology" by Zomorodian and Carlsson.
BooleanClassicalHomology(Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.BooleanClassicalHomology: This constructor initializes the object with a comparator on the basis type.
BooleanPersistenceAlgorithm - Class in edu.stanford.math.plex4.autogen.homology: This class defines the functionality for a persistence algorithm with underlying field type being boolean and underlying basis element type being U.
BooleanPersistenceAlgorithm(Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This constructor initializes the object with a comparator on the basis type.
BooleanPersistentHomology - Class in edu.stanford.math.plex4.autogen.homology: This class defines the functionality for a persistence algorithm with underlying field type being boolean and underlying basis element type being U.
BooleanPersistentHomology(Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.BooleanPersistentHomology: This constructor initializes the object with a comparator on the basis type.
BooleanRelativeHomology - Class in edu.stanford.math.plex4.autogen.homology
BooleanRelativeHomology(Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.BooleanRelativeHomology: This constructor initializes the object with a comparator on the basis type.
bottleneck - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
BottleneckDistance - Class in edu.stanford.math.plex4.bottleneck
BottleneckDistance() - Constructor for class edu.stanford.math.plex4.bottleneck.BottleneckDistance
boundary(int) - Method in class edu.stanford.math.plex.Simplex: Return the boundary of a simplex as a chain over a given characteristic.
boundaryArray() - Method in class edu.stanford.math.plex.Packed2Simplex: Returns the boundary of self.
boundaryArray() - Method in class edu.stanford.math.plex.Packed4Simplex: Returns the boundary of self.
boundaryArray() - Method in class edu.stanford.math.plex.Packed6Simplex: Returns the boundary of self.
boundaryArray() - Method in class edu.stanford.math.plex.Packed8Simplex: Returns the boundary of self.
boundaryArray() - Method in class edu.stanford.math.plex.Simplex: Return an array of simplices that describes the boundary.
boundaryMatrix(SimplexStream, double, int) - Static method in class edu.stanford.math.plex.PersistenceBasis: Returns a boundary matrix for a given simple simplex stream in a format usable from Matlab.
boundaryMatrixSparse(SimplexStream, double, int) - Static method in class edu.stanford.math.plex.PersistenceBasis: Returns a sparse boundary matrix for a given simple simplex stream in a format usable from Matlab.
BoundedIntervalCover - Class in edu.stanford.math.mapper
BoundedIntervalCover(double, double, int, double) - Constructor for class edu.stanford.math.mapper.BoundedIntervalCover
bsh - package bsh
bsh.commands - package bsh.commands
buf_is_consistent(DoubleBuffer, int, boolean) - Method in class edu.stanford.math.plex.MappedBufferData
bufferedImage - Variable in class edu.stanford.math.plex.BCPlot
BufferedImageWriter - Class in edu.stanford.math.plex4.io

C

C - Variable in class edu.stanford.math.plex.ExplicitStream.DComplex
C() - Method in class edu.stanford.math.plex.ExplicitStream.DComplex: Return the array of vertex arrays for the simplices of this dimension.
C - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
cachedTracker - Variable in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
capacity - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
Cell - Class in edu.stanford.math.plex4.homology.chain_basis: This class implements the functionality of a cell within a CW complex.
Cell() - Constructor for class edu.stanford.math.plex4.homology.chain_basis.Cell: This constructor initializes the cell to be a 0-cell (a vertex), with the default cellId as the vertex index.
Cell(int, Collection<Cell>) - Constructor for class edu.stanford.math.plex4.homology.chain_basis.Cell: This constructor initializes a cell to be an n-cell with n > 0.
Cell(int, Collection<Cell>, int[]) - Constructor for class edu.stanford.math.plex4.homology.chain_basis.Cell: This constructor initializes the cell to be an n-cell with n > 0.
Cell(int, Cell[]) - Constructor for class edu.stanford.math.plex4.homology.chain_basis.Cell: This constructor initializes a cell to be an n-cell with n > 0.
CellComparator - Class in edu.stanford.math.plex4.homology.chain_basis: This class provides functionality for comparing two cells within a CW complex.
CellComplexOperations - Class in edu.stanford.math.plex4.examples: This class contains utility functions for working with cell complexes.
CellComplexOperations() - Constructor for class edu.stanford.math.plex4.examples.CellComplexOperations
CellStreamExamples - Class in edu.stanford.math.plex4.examples: This class contains various static functions for producing cell complexes.
CellStreamExamples() - Constructor for class edu.stanford.math.plex4.examples.CellStreamExamples
centerText(String, Font, FontMetrics, Color, String, Font, FontMetrics, Color, Graphics, int, int, int, int, double) - Method in class edu.stanford.math.plex.BCPlot.DrawingPane: Center text to be displayed within a given rectangle
Chain - Class in edu.stanford.math.plex: A Chain instance is an element of the module constructed by taking formal sums of ring elements times simplices.
Chain(int, int[], Simplex[]) - Constructor for class edu.stanford.math.plex.Chain
Chain(int) - Constructor for class edu.stanford.math.plex.Chain
Chain(int, int, Simplex) - Constructor for class edu.stanford.math.plex.Chain
chain() - Method in class edu.stanford.math.plex.Simplex: Get the chain value.
chain_sort(Simplex[], int[]) - Static method in class edu.stanford.math.plex.Chain
chainModule - Variable in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This objects performs the chain computations.
chainModule - Variable in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This objects performs the chain computations.
chainModule - Variable in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This objects performs the chain computations.
chainModule - Variable in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This objects performs the chain computations.
chainModule - Variable in class edu.stanford.math.plex4.homology.zigzag.bootstrap.VietorisRipsBootstrapper
chainModule - Variable in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
chainModule - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker: These objects performs the chain computations.
chainModule - Variable in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker: This objects performs the chain computations.
chainModule - Variable in class edu.stanford.math.plex4.homology.zigzag.ZigZagHomology: This objects performs the chain computations.
chainVector(SimplexStream, Chain, double) - Static method in class edu.stanford.math.plex.PersistenceBasis
check_2_vertices(int[]) - Static method in class edu.stanford.math.plex.Packed2Simplex
check_4_vertices(int[]) - Static method in class edu.stanford.math.plex.Packed4Simplex
check_6_vertices(int[]) - Static method in class edu.stanford.math.plex.Packed6Simplex
check_8_vertices(int[]) - Static method in class edu.stanford.math.plex.Packed8Simplex
checkConsistency - Static variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
checkInvariant() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
checkReduced(Map<X, IntSparseFormalSum<Y>>, Comparator<Y>) - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
CIRCLE_SIZE - Static variable in class edu.stanford.math.plex.BCPlot
CircleGraph - Class in edu.stanford.math.plex4.graph.random: Class that represents a graph with a circle "shape"
CircleGraph(int, int, double) - Constructor for class edu.stanford.math.plex4.graph.random.CircleGraph
clearChain() - Method in class edu.stanford.math.plex.Simplex: Clear the chain value; used when we reuse the elementes in a stream.
close() - Method in class edu.stanford.math.plex.ExplicitStream: Close the stream the current additions, provided that the contents are consistent and complete.
close() - Method in class edu.stanford.math.plex4.io.MatlabWriter: This function flushes the output stream and closes it.
closed - Variable in class edu.stanford.math.plex.ExplicitStream
ClusteredERGraph - Class in edu.stanford.math.plex4.graph.random: Makes a clustered graph by connecting a specified number of clusters (i.e.
ClusteredERGraph(int) - Constructor for class edu.stanford.math.plex4.graph.random.ClusteredERGraph
coboundary - Variable in class edu.stanford.math.plex.PersistenceBasis.ListItem
cocycle - Variable in class edu.stanford.math.plex.PersistenceBasis.ListItem
coefficientOf(Simplex) - Method in class edu.stanford.math.plex.Chain
collapse(AbstractMultifilteredStream<T>) - Method in interface edu.stanford.math.plex4.streams.multi.AbstractStreamFlattener
collapse(AbstractMultifilteredStream<T>) - Method in class edu.stanford.math.plex4.streams.multi.HalfplaneFlattener
collapse(AbstractMultifilteredStream<T>) - Method in class edu.stanford.math.plex4.streams.multi.IncreasingOrthantFlattener
CollectionUtility - Class in edu.stanford.math.plex4.utility
CollectionUtility() - Constructor for class edu.stanford.math.plex4.utility.CollectionUtility
colors - Static variable in class edu.stanford.math.plex4.visualization.AbstractVisualizer
columnHeadings - Variable in class edu.stanford.math.plex4.io.Table
commonAncestorDepth(int, int) - Method in class edu.stanford.math.plex4.graph.random.BinaryTree
comp_sort(int[], int, int, PlexSort.Comp) - Static method in class edu.stanford.math.plex.PlexSort: Sort a subarray of an int[] using a comparison function.
comp_sort(long[], int, int, PlexSort.CompL) - Static method in class edu.stanford.math.plex.PlexSort: Same as comp_sort(int[], int, int, Comp), but for arrays of long.
comp_sort(Object[], int, int, PlexSort.CompObj) - Static method in class edu.stanford.math.plex.PlexSort: Same as comp_sort(int[], int, int, Comp), but for arrays of Object.
compare(Interval<Double>, Interval<Double>) - Method in class edu.stanford.math.plex4.homology.barcodes.IntervalLengthComparator
compare(Cell, Cell) - Method in class edu.stanford.math.plex4.homology.chain_basis.CellComparator
compare(Simplex, Simplex) - Method in class edu.stanford.math.plex4.homology.chain_basis.SimplexComparator
compare(SimplexPair, SimplexPair) - Method in class edu.stanford.math.plex4.homology.chain_basis.SimplexPairComparator
compare(M, M) - Method in class edu.stanford.math.plex4.streams.utility.FilteredComparator
compareDoublesAbsolute(double, double, double) - Static method in class edu.stanford.math.plex4.utility.ComparisonUtility: This function compares two doubles to see if they are within the specified tolerance of each other.
compareDoublesGuardedRelative(double, double, double) - Static method in class edu.stanford.math.plex4.utility.ComparisonUtility: This function compares two doubles to see if their (relative/absolute) distance is within the specified tolerance.
compareDoublesRelative(double, double, double) - Static method in class edu.stanford.math.plex4.utility.ComparisonUtility: This function compares two doubles to see if their relative distance is within the specified tolerance.
compareIntArrays(int[], int[]) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility: This function performs a comparison of two arrays of ints.
compareTo(Packed2Simplex) - Method in class edu.stanford.math.plex.Packed2Simplex
compareTo(Simplex) - Method in class edu.stanford.math.plex.Packed2Simplex: Implements Comparable interface.
compareTo(Packed4Simplex) - Method in class edu.stanford.math.plex.Packed4Simplex
compareTo(Simplex) - Method in class edu.stanford.math.plex.Packed4Simplex: Implements Comparable interface.
compareTo(Packed6Simplex) - Method in class edu.stanford.math.plex.Packed6Simplex
compareTo(Simplex) - Method in class edu.stanford.math.plex.Packed6Simplex: Implements Comparable interface.
compareTo(Packed8Simplex) - Method in class edu.stanford.math.plex.Packed8Simplex
compareTo(Simplex) - Method in class edu.stanford.math.plex.Packed8Simplex: Implements Comparable interface.
compareTo(PersistenceBasisInterval) - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Float: Implements Comparable interface.
compareTo(PersistenceBasisInterval) - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Int: Implements Comparable interface.
compareTo(PersistenceInterval) - Method in class edu.stanford.math.plex.PersistenceInterval.Float: Implements Comparable interface.
compareTo(PersistenceInterval) - Method in class edu.stanford.math.plex.PersistenceInterval.Int: Implements Comparable interface.
compareTo(Simplex) - Method in class edu.stanford.math.plex.Simplex: Implements Comparable interface.
compareTo(Interval<T>) - Method in class edu.stanford.math.plex4.homology.barcodes.Interval
compareTo2(Interval<T>) - Method in class edu.stanford.math.plex4.homology.barcodes.Interval
ComparisonUtility - Class in edu.stanford.math.plex4.utility: This class contains static methods for comparing various objects.
ComparisonUtility() - Constructor for class edu.stanford.math.plex4.utility.ComparisonUtility
computeAnnotatedIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm
computeAnnotatedIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm
computeAnnotatedIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm
computeAnnotatedIndexIntervals(AbstractFilteredStream<T>) - Method in class edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceBasisAlgorithm: This function computes the augmented persistence index intervals for a supplied filtered chain complex.
computeAnnotatedIntervals(AbstractFilteredStream<T>) - Method in class edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceBasisAlgorithm: This function computes the augmented persistence intervals for a supplied filtered chain complex.
computeAnnotatedIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This function provides the implementation of computeAnnotatedIntervals.
computeAnnotatedIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistentHomology
computeAnnotatedIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This function provides the implementation of computeAnnotatedIntervals.
computeAnnotatedIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistentHomology
computeAnnotatedIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This function provides the implementation of computeAnnotatedIntervals.
computeAnnotatedIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistentHomology
computeBottleneckDistance(List<Interval<Double>>, List<Interval<Double>>) - Static method in class edu.stanford.math.plex4.bottleneck.BottleneckDistance
computeBoundary(IntSparseFormalSum<X>, IntAlgebraicFreeModule<X>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function computes the boundary of a given chain, by linear extension.
computeCentroid(AbstractObjectMetricSpace<double[]>) - Static method in class edu.stanford.math.plex4.metric.utility.MetricUtility: This function computes the centroid of the set of points within the metric space.
computeCone(AbstractFilteredStream<Simplex>, int) - Static method in class edu.stanford.math.plex4.examples.SimplicialComplexOperations: This function computes the cone of a given filtered simplicial complex.
computeDisjointUnion(AbstractFilteredStream<Simplex>, AbstractFilteredStream<Simplex>) - Static method in class edu.stanford.math.plex4.examples.SimplicialComplexOperations: This function computes the disjoint union of two filtered simplicial complex.
computeIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanClassicalHomology
computeIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm
computeIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntClassicalHomology
computeIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm
computeIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectClassicalHomology
computeIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm
computeIndexIntervals(AbstractFilteredStream<T>) - Method in class edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceAlgorithm: This function computes the persistence index intervals of a filtered chain complex.
computeIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype
computeIndexIntervals(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.homology.zigzag.ZigZagHomology
computeIndexIntervals(AbstractFilteredStream<Simplex>) - Method in class edu.stanford.math.plex4.interop.Plex3PersistenceAlgorithm
computeInducedFiltrationValue(double, double) - Method in class edu.stanford.math.plex4.homology.filtration.ExternalConverter
computeInducedFiltrationValue(double, double) - Method in class edu.stanford.math.plex4.homology.filtration.FiltrationConverter: This function computes the filtration value that is consistent with the ordering of filtration indices.
computeInducedFiltrationValue(double, double) - Method in class edu.stanford.math.plex4.homology.filtration.IdentityConverter
computeInducedFiltrationValue(double, double) - Method in class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter
computeInducedFiltrationValue(double, double) - Method in class edu.stanford.math.plex4.homology.filtration.StaticConverter
computeInducedMap(AbstractPersistenceTracker<K1, I1, G1>, AbstractHomologyTracker<K2, I2, ?, G2>, IntAbstractModule<G2>, ObjectObjectFunction<G1, G2>) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.InducedHomologyMappingUtility
computeIntersection(TIntHashSet, TIntHashSet) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility: This function computes the intersection between two sets of integers.
computeIntervals(SimplexStream) - Method in class edu.stanford.math.plex.Persistence: Calculate the persistent homology.
computeIntervals(SimplexStream, boolean, int) - Method in class edu.stanford.math.plex.Persistence: Calculate the persistent homology with a specified Zp.
computeIntervals(SimplexStream) - Static method in class edu.stanford.math.plex.PersistenceBasis: Compute the persistent homology intervals of the simplex stream given.
computeIntervals(SimplexStream, boolean) - Static method in class edu.stanford.math.plex.PersistenceBasis: Compute the persistent homology intervals of the simplex stream given with an option flag to control which type of basis we want to choose.
computeIntervals(SimplexStream, int, boolean) - Method in class edu.stanford.math.plex.PersistenceBasis: Compute the persistent homology intervals of the simplex stream given with explicitly given characteristic of the underlying field as well as an option flag to control which type of basis we want to choose.
computeIntervals(AbstractFilteredStream<T>) - Method in class edu.stanford.math.plex4.homology.interfaces.AbstractPersistenceAlgorithm: This function computes the persistence intervals of a filtered chain complex.
computeIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This function provides the implementation of computeIntervals.
computeIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistentHomology
computeIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This function provides the implementation of computeIntervals.
computeIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistentHomology
computeIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This function provides the implementation of computeIntervals.
computeIntervalsImpl(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistentHomology
computeLandmarkSet() - Method in class edu.stanford.math.plex4.metric.landmark.ExplicitLandmarkSelector
computeLandmarkSet() - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector: This function constructs the set of landmark points.
computeLandmarkSet() - Method in class edu.stanford.math.plex4.metric.landmark.MaxMinLandmarkSelector
computeLandmarkSet() - Method in class edu.stanford.math.plex4.metric.landmark.RandomLandmarkSelector
computeMaxima(AbstractObjectMetricSpace<double[]>) - Static method in class edu.stanford.math.plex4.metric.utility.MetricUtility: This function computes the coordinate-wise maxima of a given Euclidean metric space.
computeMaximumCardinalityMatching() - Method in class edu.stanford.math.plex4.bottleneck.WeightedBipartiteGraph
computeMinima(AbstractObjectMetricSpace<double[]>) - Static method in class edu.stanford.math.plex4.metric.utility.MetricUtility: This function computes the coordinate-wise minima of a given Euclidean metric space.
computePerfectMatchingThreshold() - Method in class edu.stanford.math.plex4.bottleneck.WeightedBipartiteGraph: This function computes the smallest value, v, that when the current bipartite graph is filtered by v, a perfect matching exists.
computePersistentCohomologyZigZag(SimplexStream, int) - Static method in class edu.stanford.math.plex.PersistenceBasis: Computes persistent cohomology using a zig-zag based approach due to Dmitriy Morozov.
computePersistentCohomologyZigZag(SimplexStream) - Static method in class edu.stanford.math.plex.PersistenceBasis
computeRawIntervals(SimplexStream, boolean, int) - Method in class edu.stanford.math.plex.Persistence: Calculate the raw persistent intervals for a stream, using a specified Zp.
computeRawIntervals(SimplexStream, int) - Method in class edu.stanford.math.plex.PersistenceBasis
computeShortestPaths(AbstractUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility: This function computes all of the distances between pairs of vertices using the Floyd-Warshall algorithm.
computeSuspension(AbstractFilteredStream<Simplex>, int) - Static method in class edu.stanford.math.plex4.examples.SimplicialComplexOperations: This function computes the suspension of a given filtered simplicial complex.
Cone - Class in edu.stanford.math.plex: The class Cone provides support for computing persistence across a filtration as well as a cone over this filtration.
Cone(SimplexStream) - Constructor for class edu.stanford.math.plex.Cone: Creates a new cone from an existing SimplexStream.
conepoint - Variable in class edu.stanford.math.plex.Cone
coning - Variable in class edu.stanford.math.plex.Cone
construct(double) - Method in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph: Construct the Hierarchical graph.
constructComplex() - Method in class edu.stanford.math.plex4.streams.impl.ExplicitStream
constructComplex() - Method in class edu.stanford.math.plex4.streams.impl.FlagComplexStream
constructComplex() - Method in class edu.stanford.math.plex4.streams.impl.WitnessBicomplex
constructComplex() - Method in class edu.stanford.math.plex4.streams.impl.WitnessStream
constructComplex() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream: This abstract function performs the construction of the filtered chain complex.
constructEdges(int, int, int, double[]) - Method in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph: Construct the edges of the graph using probabilities in the array probs.
constructEdges() - Method in class edu.stanford.math.plex4.streams.impl.FlagComplexStream: This function implements the construction of the 1-skeleton.
constructEdges() - Method in class edu.stanford.math.plex4.streams.impl.FlexibleVietorisRipsStream
constructEdges() - Method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
contains(Iterable<T>, T) - Method in class edu.stanford.math.plex4.bottleneck.FlowNetwork
contains(int[], int) - Static method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
containsActiveInterval(K) - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
containsEdge(int, int) - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph: This function returns true if the edge (i, j) is in the graph, and false otherwise.
containsEdge(int, int) - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph
containsEdge(int, int) - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
containsElement(Simplex) - Method in class edu.stanford.math.plex4.interop.Plex3Stream
containsElement(T) - Method in class edu.stanford.math.plex4.streams.derived.DualStream
containsElement(ObjectObjectPair<T, U>) - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
containsElement(T) - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
containsElement(T) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitStream: This function returns true if the stream contains the query element.
containsElement(Simplex) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
containsElement(T) - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function returns whether an element is contained in the stream.
containsElement(T) - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
containsElement(T) - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
containsElement(T) - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
containsElement(T) - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function returns true if the stream contains the given basis element, and false otherwise.
containsPoint(T) - Method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function determines whether the given point is a member of the interval.
context - Variable in class edu.stanford.math.plex.PlexMessageWindow
convert_filtration_index(int) - Method in class edu.stanford.math.plex.ExplicitStream: Convert a filtration index into a persistence parameter (i.e., double) -- gets overloaded by some subclasses.
convert_filtration_index(int) - Method in class edu.stanford.math.plex.LazyWitnessStream: Convert a filtration index into a persistence parameter (i.e., double) -- gets overloaded by some subclasses.
convert_filtration_index(int) - Method in class edu.stanford.math.plex.RipsStream: Convert a filtration index into a persistence parameter (i.e., double) -- gets overloaded by some subclasses.
convert_filtration_index(int) - Method in class edu.stanford.math.plex.SimplexStream: Convert a filtration index into a persistence parameter (i.e., double) -- gets overloaded by some subclasses.
convert_filtration_index(int) - Method in class edu.stanford.math.plex.WitnessStream: Convert a filtration index into a persistence parameter (i.e., double) -- gets overloaded by some subclasses.
converter - Variable in class edu.stanford.math.plex4.streams.impl.FlagComplexStream: This converts between filtration indices and values
converter - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream: This converts between filtration indices and values
convertIndices(Simplex, int[]) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility
convertIndices(int[], int[]) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility
convertInterval(PersistenceInterval) - Method in class edu.stanford.math.plex.SimplexStream: Convert a PersistenceInterval into Float format in a stream-specific manner.
convertInterval(PersistenceBasisInterval) - Method in class edu.stanford.math.plex.SimplexStream: convert a PersistenceBasisInterval into Float format in a stream-specific manner.
coordinate(int, int) - Method in class edu.stanford.math.plex.EuclideanArrayData: Get coordinates.
coordinate(int, int) - Method in class edu.stanford.math.plex.MappedBufferData: Get coordinates.
coordinate(int, int) - Method in class edu.stanford.math.plex.PointData.NSpace
coordinate(int, int) - Method in class edu.stanford.math.plex.Torus: i-th coordinate of point p;
copy() - Method in class edu.stanford.math.plex.Packed2Simplex: Make a "blank" copy of the Simplex -- equivalent to getSimplex(this.vertices()).
copy() - Method in class edu.stanford.math.plex.Packed4Simplex: Make a "blank" copy of the Simplex -- equivalent to getSimplex(this.vertices()).
copy() - Method in class edu.stanford.math.plex.Packed6Simplex: Make a "blank" copy of the Simplex -- equivalent to getSimplex(this.vertices()).
copy() - Method in class edu.stanford.math.plex.Packed8Simplex: Make a "blank" copy of the Simplex -- equivalent to getSimplex(this.vertices()).
copy() - Method in class edu.stanford.math.plex.Simplex: Make a "blank" copy of the Simplex -- equivalent to getSimplex(this.vertices()).
copy() - Method in class edu.stanford.math.plex.SimplexStream.Head
copyOf(double[], int) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
copyOf(int[], int) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
copyOf(float[], int) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
copyOf(short[], int) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
copyOf(long[], int) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
copyOf(boolean[], int) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
copyOf(byte[], int) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
copyOf(char[], int) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
copyOf(Object[], int) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
correctBettiSequence() - Method in class edu.stanford.math.plex4.graph.random.CircleGraph
count() - Method in class edu.stanford.math.plex.DiscreteSpace: The number of data points.
count() - Method in class edu.stanford.math.plex.DistanceData: The number of data points.
count() - Method in class edu.stanford.math.plex.EuclideanArrayData: The number of data points.
count() - Method in class edu.stanford.math.plex.MappedBufferData: The number of data points.
count() - Method in class edu.stanford.math.plex.PointData: The number of points in this data set.
count() - Method in class edu.stanford.math.plex.PointData.Discrete: The number of points in this data set.
count() - Method in class edu.stanford.math.plex.RDirectBufferData
count() - Method in class edu.stanford.math.plex.Torus: The number of data points.
counter - Variable in class edu.stanford.math.plex.SimplexFaceIterator
CRC - Class in edu.stanford.math.plex: The CRC class provides good hash methods for int/long and string data.
create() - Static method in class edu.stanford.math.mapper.MapperSpecifier
createAlexanderWhitneyMatrix(AbstractFilteredStream<Simplex>) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility
createBarcodePlot(PersistenceInvariantDescriptor<Interval<Double>, G>, String, double) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates an images of a collection of barcodes and writes it to a file.
createBoundaryMatrixAsDoubleSum(AbstractFilteredStream<T>) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function returns the boundary matrix for the entire complex.
createBoundaryMatrixAsDoubleSum(AbstractFilteredStream<T>, int) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function returns the boundary matrix for the entire complex.
createBoundaryMatrixAsIntSum(AbstractFilteredStream<T>) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function returns the boundary matrix for the entire complex.
createBoundaryMatrixAsIntSum(AbstractFilteredStream<T>, int) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function returns the boundary matrix for the entire complex.
createEuclideanMetricSpace(double[][]) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new EuclideanMetricSpace object.
createExplicitCellStream() - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createExplicitCellStream(double) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createExplicitCellStream() - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new ExplicitCellStream object.
createExplicitCellStream(double) - Static method in class edu.stanford.math.plex4.api.Plex4
createExplicitSelector(double[][], int[]) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new explicit landmark selector on a point cloud.
createExplicitSelector(AbstractSearchableMetricSpace<T>, int[]) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new explicit landmark selector on an abstract metric space.
createExplicitSimplexStream() - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createExplicitSimplexStream(double) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createExplicitSimplexStream() - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new ExplicitSimplexStream object.
createExplicitSimplexStream(double) - Static method in class edu.stanford.math.plex4.api.Plex4
createGraphComplex(AbstractUndirectedGraph) - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function produces a simplicial complex from a given undirected graph.
createGraphComplex(int[][]) - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function produces a simplicial complex from the adjacency matrix of a given graph.
createGraphics(BufferedImage) - Static method in class edu.stanford.math.plex4.visualization.BarcodeVisualizer
createHomMatrixConverter(AbstractFilteredStream<Simplex>, AbstractFilteredStream<Simplex>) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a matrix converter object for converting between formal sums, sparse and dense matrices.
createHomStream(AbstractFilteredStream<T>, AbstractFilteredStream) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new hom stream from two given filtered streams.
createLazyWitnessStream(LandmarkSelector<double[]>, int, double, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function create a new lazy-witness stream given a point cloud.
createLazyWitnessStream(LandmarkSelector<double[]>, int, double) - Static method in class edu.stanford.math.plex4.api.Plex4: This function create a new lazy-witness stream given a point cloud.
createMatrixConverter(AbstractFilteredStream<Simplex>) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a vector converter for converting between formal sums, and sparse and dense arrays.
createMaxMinSelector(double[][], int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new max-min landmark selector on a point cloud.
createMaxMinSelector(double[][], int, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new max-min landmark selector on a point cloud.
createMaxMinSelector(AbstractSearchableMetricSpace<T>, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new max-min landmark selector on an abstract metric space.
createMaxMinSelector(AbstractSearchableMetricSpace<T>, int, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new max-min landmark selector on an abstract metric space.
createMenuBar() - Method in class edu.stanford.math.plex.BCPlot
createMetricSpace(AbstractUndirectedGraph) - Method in interface edu.stanford.math.plex4.graph.metric.GraphMetricFactory: This function produces a finite metric space on the vertex set of a given graph.
createMetricSpace(AbstractUndirectedGraph) - Method in class edu.stanford.math.plex4.graph.metric.ShortestPathMetric
createNewSum(int[], PrimitiveBasisElement[]) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function creates a new formal sum from the given set of coefficients and objects.
createPair(Simplex, Simplex) - Static method in class edu.stanford.math.plex4.homology.chain_basis.SimplexPair
createPair(int, int) - Static method in class edu.stanford.math.plex4.homology.chain_basis.SimplexPair
createPair(int[], int[]) - Static method in class edu.stanford.math.plex4.homology.chain_basis.SimplexPair
createPlex3LazyWitnessStream(LandmarkSelector<double[]>, int, double, int) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createPlex3VietorisRipsStream(double[][], int, double, int) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createPlex3WitnessStream(LandmarkSelector<double[]>, int, double, int) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createPlex4LazyWitnessStream(LandmarkSelector<double[]>, int, double, int) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createPlex4VietorisRipsStream(double[][], int, double, int) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createPlex4VietorisRipsStream(AbstractSearchableMetricSpace<T>, int, double, int) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createPlex4VietorisRipsStream(double[][], int, double[]) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createPlex4VietorisRipsStream(AbstractSearchableMetricSpace<T>, int, double[]) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createPlex4WitnessStream(LandmarkSelector<double[]>, int, double, int) - Static method in class edu.stanford.math.plex4.api.FilteredStreamInterface
createRandomSelector(double[][], int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new random landmark point selector on a point cloud.
createRandomSelector(AbstractSearchableMetricSpace<T>, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a new randomized landmark selector on an abstract metric space.
createSubMetricSpace(AbstractIntMetricSpace, int[]) - Static method in class edu.stanford.math.mapper.MetricUtility
createSubMetricSpace(AbstractIntMetricSpace, TIntHashSet) - Static method in class edu.stanford.math.mapper.MetricUtility
createUniformIntervalCover(IntFilterFunction, int, double) - Static method in class edu.stanford.math.mapper.RangeCoverUtility
createVietorisRipsStream(double[][], int, double, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a Vietoris-Rips complex given a point cloud.
createVietorisRipsStream(double[][], int, double) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a Vietoris-Rips complex given a point cloud.
createVietorisRipsStream(AbstractSearchableMetricSpace<T>, int, double, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a Vietoris-Rips complex from a metric space.
createVietorisRipsStream(AbstractSearchableMetricSpace<T>, int, double) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a Vietoris-Rips complex given a metric space.
createVietorisRipsStream(double[][], int, double[]) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a Vietoris-Rips complex given a point cloud.
createVietorisRipsStream(AbstractSearchableMetricSpace<T>, int, double[]) - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a Vietoris-Rips complex from a metric space.
createWitnessStream(LandmarkSelector<double[]>, int, double) - Static method in class edu.stanford.math.plex4.api.Plex4: This function create a new witness stream given a point cloud.
createWitnessStream(LandmarkSelector<double[]>, int, double, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function create a new witness stream given a point cloud.
current - Variable in class edu.stanford.math.plex.SimplexFaceIterator
current - Variable in class edu.stanford.math.plex.SimplexStream.Stack.Segment
current_count - Variable in class edu.stanford.math.plex.SimplexTable.SimpleTableIterator
current_dimension - Variable in class edu.stanford.math.plex.ExplicitStream
current_dimension - Variable in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
current_index - Variable in class edu.stanford.math.plex.ExplicitStream
current_index - Variable in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
current_index - Variable in class edu.stanford.math.plex.SimplexTable.SimpleTableIterator
current_seg - Variable in class edu.stanford.math.plex.SimplexStream.Stack.StackIterator
cycleSpaceDimension() - Method in class edu.stanford.math.plex.Persistence: Return the dimension of the cycle space.

D

D - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
D - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream
d_okay(double[][]) - Static method in class edu.stanford.math.plex.Plex
data() - Method in class edu.stanford.math.plex.PointData.Predicate: Underlying PointData for the predicate.
debug(String) - Method in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
debugFlag - Variable in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
deconvertIndices(int[], int[]) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility
decrement_findex() - Method in class edu.stanford.math.plex.Simplex: Decrement the findex value -- this is a hack that should ONLY be used if you know what you are doing.
deepArrayCopy(Object) - Static method in class edu.stanford.math.plex4.utility.MemoryUtility
DEFAULT_BARS_PER_PAGE - Static variable in class edu.stanford.math.plex.BCPlot
DEFAULT_WIDTH - Static variable in class edu.stanford.math.plex4.visualization.BarcodeVisualizer
defineCluster(int, int, double) - Method in class edu.stanford.math.plex4.graph.random.ClusteredERGraph: Warning: No input validation is performed.
degreeSequence - Variable in class edu.stanford.math.plex4.graph.random.PrescribedDegrees
delete(String) - Static method in class edu.stanford.math.plex.MappedBufferData
delta_minus - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
delta_minus - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonNode
delta_plus - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
delta_plus - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonNode
DensityEstimation - Class in edu.stanford.math.plex4.metric.utility
DensityEstimation() - Constructor for class edu.stanford.math.plex4.metric.utility.DensityEstimation
DeSilvaMorozovJohanssonExample<R> - Class in edu.stanford.math.plex4.examples: This class contains the cell complex example contained in the paper "Dualities in persistent (co)homology" by Vin de Silva, Dmitriy Morozov and Mikael Vejdemo-Johansson.
DeSilvaMorozovJohanssonExample(ObjectAbstractField<R>) - Constructor for class edu.stanford.math.plex4.examples.DeSilvaMorozovJohanssonExample: This constructor initializes the class with the specified field.
DIM_0_MASK - Static variable in class edu.stanford.math.plex.Packed2Simplex
DIM_2_MASK - Static variable in class edu.stanford.math.plex.Packed4Simplex
DIM_4_MASK - Static variable in class edu.stanford.math.plex.Packed6Simplex
DIM_6_MASK - Static variable in class edu.stanford.math.plex.Packed8Simplex
dimension() - Method in class edu.stanford.math.plex.EuclideanArrayData: The number of dimensions of the space.
dimension - Variable in class edu.stanford.math.plex.ExplicitStream.DComplex
dimension() - Method in class edu.stanford.math.plex.ExplicitStream.DComplex: Return the dimension of this DComplex.
dimension() - Method in class edu.stanford.math.plex.MappedBufferData: The number of dimensions of the space.
dimension() - Method in class edu.stanford.math.plex.Packed2Simplex: Returns the dimension of self.
dimension() - Method in class edu.stanford.math.plex.Packed4Simplex: Returns the dimension of self.
dimension() - Method in class edu.stanford.math.plex.Packed6Simplex: Returns the dimension of self.
dimension() - Method in class edu.stanford.math.plex.Packed8Simplex: Returns the dimension of self.
dimension - Variable in class edu.stanford.math.plex.PersistenceBasisInterval: The dimension of the PersistenceBasisInterval.
dimension - Variable in class edu.stanford.math.plex.PersistenceInterval: The dimension of the PersistenceInterval.
dimension() - Method in class edu.stanford.math.plex.PointData.NSpace: Dimension of the space.
dimension() - Method in class edu.stanford.math.plex.Simplex: Returns the dimension of self.
dimension() - Method in class edu.stanford.math.plex.Torus: The number of dimensions of the space.
dimension - Variable in class edu.stanford.math.plex4.graph.random.RandomGeometricGraph
dimension - Variable in class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
dimension_bound - Variable in class edu.stanford.math.plex.SimplexStream.Stack
dimension_bound - Variable in class edu.stanford.math.plex.SimplexStream.Stack.StackIterator
disableLogging() - Method in class bsh.PlexInterpreter: Turn OFF input logging for this Interpreter.
DiscreteSpace - Class in edu.stanford.math.plex: The DiscreteSpace class implements a finite discrete metric space.
DiscreteSpace(int) - Constructor for class edu.stanford.math.plex.DiscreteSpace
DisjointSetSystem - Class in edu.stanford.math.clustering
DisjointSetSystem(int) - Constructor for class edu.stanford.math.clustering.DisjointSetSystem
DisjointSetSystem - Class in edu.stanford.math.plex4.homology.nonautogen: Deprecated.
DisjointSetSystem(int) - Constructor for class edu.stanford.math.plex4.homology.nonautogen.DisjointSetSystem: Deprecated.
DisjointSetSystem(DisjointSetSystem) - Constructor for class edu.stanford.math.plex4.homology.nonautogen.DisjointSetSystem: Deprecated.
disjointUnion(ExplicitCellStream, ExplicitCellStream) - Static method in class edu.stanford.math.plex4.examples.CellComplexOperations: This function produces a cell complex that is the disjoint union of two cell complexes.
dist - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonNode
dist_sort(double[]) - Static method in class edu.stanford.math.plex.Simplex: Sort an array of double into increasing order, as needed for some Simplex operations.
distance(int, int) - Method in class edu.stanford.math.plex.DiscreteSpace: Discrete distance.
distance(int, int) - Method in class edu.stanford.math.plex.DistanceData: Euclidean distance.
distance(int, int) - Method in class edu.stanford.math.plex.EuclideanArrayData: Euclidean distance.
distance(int, int) - Method in class edu.stanford.math.plex.MappedBufferData: Euclidean distance.
distance(int, int) - Method in class edu.stanford.math.plex.PointData.Discrete: Distance between 2 points.
distance(int, int) - Method in class edu.stanford.math.plex.PointData: Distance between 2 points.
distance(int, int) - Method in class edu.stanford.math.plex.RDirectBufferData: Return the distance between the two points using the external data, which is stored as 0-based columns.
distance(int, int) - Method in class edu.stanford.math.plex.Torus: Toroidal distance.
distance(double[], double[]) - Method in class edu.stanford.math.plex4.graph.random.KNearestNeighborsGraph
distance(double[], double[]) - Method in class edu.stanford.math.plex4.graph.random.ManifoldGraph: This function must implement the distance function on the manifold.
distance(double[], double[]) - Method in class edu.stanford.math.plex4.graph.random.RandomGeometricGraph
distance(double[], double[]) - Method in class edu.stanford.math.plex4.graph.random.SphereGraph
distance(double[], double[]) - Method in class edu.stanford.math.plex4.graph.random.TorusGraph
distance(double[], double[]) - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
distance(int, int) - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
distance(double[], double[]) - Method in class edu.stanford.math.plex4.metric.impl.EuclideanMetricSpace
distance(int, int) - Method in class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace
distance(Integer, Integer) - Method in class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace
distance(T, T) - Method in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace
distance(int, int) - Method in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace
distance(int, int) - Method in interface edu.stanford.math.plex4.metric.interfaces.AbstractIntMetricSpace: This function returns the distance between the object at index i and the object at index j.
distance(T, T) - Method in interface edu.stanford.math.plex4.metric.interfaces.AbstractObjectMetric: This function returns the distance between two points.
distance(int, int) - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
distance(T, T) - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
distance(int, int) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
distance(double[], double[]) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
distance(int, int) - Method in class edu.stanford.math.plex4.streams.utility.SkeletalMetric
distance(Simplex, Simplex) - Method in class edu.stanford.math.plex4.streams.utility.SkeletalMetric
distanceBuffer - Variable in class edu.stanford.math.plex.RDirectBufferData
DistanceData - Class in edu.stanford.math.plex: The DistanceData class is the simplest implementation of NSpace.
DistanceData(double[][]) - Constructor for class edu.stanford.math.plex.DistanceData
DistanceData(double[][]) - Static method in class edu.stanford.math.plex.Plex: Create a DistanceData instance.
document - Variable in class edu.stanford.math.plex.PlexMessageWindow
doDraw2D() - Method in class edu.stanford.math.plex4.visualization.AbstractVisualizer: Draw the 2D plot; i.e.
doDraw2D() - Method in class edu.stanford.math.plex4.visualization.PAppletSplitscreen: Overwrite this method to draw 2D objects in your sketch.
doDraw3D() - Method in class edu.stanford.math.plex4.visualization.AbstractVisualizer: Draws point cloud and the Vietoris Rips cpx up to current filtration value
doDraw3D() - Method in class edu.stanford.math.plex4.visualization.PAppletSplitscreen: Overwrite this method to draw 3D objects in your sketch.
doPlot(String, double[][], double) - Static method in class edu.stanford.math.plex.BCPlot: Make a barcode plot -- call via Plex.plot().
doScatter(String, double[][], double) - Static method in class edu.stanford.math.plex.BCPlot: Make a barcode scatterplot -- call via Plex.scatter().
doSetup() - Method in class edu.stanford.math.plex4.visualization.AbstractVisualizer
doSetup() - Method in class edu.stanford.math.plex4.visualization.PAppletSplitscreen: Overwrite this method to setup additional variables
dotProduct(double[], double[]) - Static method in class edu.stanford.math.plex4.utility.MathUtility
DoubleArrayReaderWriter - Class in edu.stanford.math.plex4.io
dp - Variable in class edu.stanford.math.plex.BCPlot.Ruler
draw() - Method in class edu.stanford.math.plex4.visualization.PAppletSplitscreen
drawBarcode(List<Interval<Double>>, String, double) - Static method in class edu.stanford.math.plex4.visualization.BarcodeVisualizer
drawBarsInPlace(Graphics2D, List<Interval<Double>>, ImageRegion.Int, int, int, double) - Static method in class edu.stanford.math.plex4.visualization.BarcodeVisualizer
drawBarsInPlace(List<Interval<Double>>, ImageRegion.Int, float, float, double) - Method in class edu.stanford.math.plex4.visualization.HomologyGeneratorVisualizer
drawGridLines(Graphics) - Method in class edu.stanford.math.plex.BCPlot.DrawingPane
drawRuler(Graphics, int) - Method in class edu.stanford.math.plex.BCPlot.DrawingPane
drawTicksInPlace(Graphics2D, ImageRegion.Int, int, double) - Static method in class edu.stanford.math.plex4.visualization.BarcodeVisualizer
drawTitleInPlace(Graphics2D, String, int, int, int, int) - Static method in class edu.stanford.math.plex4.visualization.BarcodeVisualizer
DSphere(int) - Static method in class edu.stanford.math.plex.PointData.Discrete: Make an instance of the boundary of the canonical (D+1)-Simplex.
DSphereKskeleton(int, int) - Static method in class edu.stanford.math.plex.PointData.Discrete
DualStream<T> - Class in edu.stanford.math.plex4.streams.derived: This class implements the dual cochain complex from a given chain complex.
DualStream(AbstractFilteredStream<T>) - Constructor for class edu.stanford.math.plex4.streams.derived.DualStream: This constructor initializes the dualized stream from the regular (forward stream).
dump(int) - Method in class edu.stanford.math.plex.ExplicitStream: Return a DComplex of the requested dimension, if there is one, else null;
dump(Iterable) - Static method in class edu.stanford.math.plex4.utility.CollectionUtility

E

EccentricityFilterFunction - Class in edu.stanford.math.plex4.streams.filter
EccentricityFilterFunction(AbstractIntMetricSpace) - Constructor for class edu.stanford.math.plex4.streams.filter.EccentricityFilterFunction
edge_length_limit - Variable in class edu.stanford.math.plex.RipsStream: The maximum length of an edge that will be admitted to the complex.
edu.stanford.math.clustering - package edu.stanford.math.clustering
edu.stanford.math.mapper - package edu.stanford.math.mapper
edu.stanford.math.plex - package edu.stanford.math.plex
edu.stanford.math.plex4.api - package edu.stanford.math.plex4.api
edu.stanford.math.plex4.autogen.homology - package edu.stanford.math.plex4.autogen.homology
edu.stanford.math.plex4.bottleneck - package edu.stanford.math.plex4.bottleneck
edu.stanford.math.plex4.examples - package edu.stanford.math.plex4.examples
edu.stanford.math.plex4.generation - package edu.stanford.math.plex4.generation
edu.stanford.math.plex4.graph - package edu.stanford.math.plex4.graph
edu.stanford.math.plex4.graph.io - package edu.stanford.math.plex4.graph.io
edu.stanford.math.plex4.graph.metric - package edu.stanford.math.plex4.graph.metric
edu.stanford.math.plex4.graph.random - package edu.stanford.math.plex4.graph.random
edu.stanford.math.plex4.graph.utility - package edu.stanford.math.plex4.graph.utility
edu.stanford.math.plex4.homology.barcodes - package edu.stanford.math.plex4.homology.barcodes
edu.stanford.math.plex4.homology.chain_basis - package edu.stanford.math.plex4.homology.chain_basis
edu.stanford.math.plex4.homology.filtration - package edu.stanford.math.plex4.homology.filtration
edu.stanford.math.plex4.homology.interfaces - package edu.stanford.math.plex4.homology.interfaces
edu.stanford.math.plex4.homology.nonautogen - package edu.stanford.math.plex4.homology.nonautogen
edu.stanford.math.plex4.homology.utility - package edu.stanford.math.plex4.homology.utility
edu.stanford.math.plex4.homology.zigzag - package edu.stanford.math.plex4.homology.zigzag
edu.stanford.math.plex4.homology.zigzag.bootstrap - package edu.stanford.math.plex4.homology.zigzag.bootstrap
edu.stanford.math.plex4.interop - package edu.stanford.math.plex4.interop
edu.stanford.math.plex4.io - package edu.stanford.math.plex4.io
edu.stanford.math.plex4.kd - package edu.stanford.math.plex4.kd
edu.stanford.math.plex4.metric.impl - package edu.stanford.math.plex4.metric.impl
edu.stanford.math.plex4.metric.interfaces - package edu.stanford.math.plex4.metric.interfaces
edu.stanford.math.plex4.metric.landmark - package edu.stanford.math.plex4.metric.landmark
edu.stanford.math.plex4.metric.utility - package edu.stanford.math.plex4.metric.utility
edu.stanford.math.plex4.streams.derived - package edu.stanford.math.plex4.streams.derived
edu.stanford.math.plex4.streams.filter - package edu.stanford.math.plex4.streams.filter
edu.stanford.math.plex4.streams.impl - package edu.stanford.math.plex4.streams.impl
edu.stanford.math.plex4.streams.interfaces - package edu.stanford.math.plex4.streams.interfaces
edu.stanford.math.plex4.streams.multi - package edu.stanford.math.plex4.streams.multi
edu.stanford.math.plex4.streams.storage_structures - package edu.stanford.math.plex4.streams.storage_structures
edu.stanford.math.plex4.streams.utility - package edu.stanford.math.plex4.streams.utility
edu.stanford.math.plex4.utility - package edu.stanford.math.plex4.utility
edu.stanford.math.plex4.visualization - package edu.stanford.math.plex4.visualization
elements - Variable in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace: This array stores the elements in the metric space
empty_dbl_file(String, int) - Static method in class edu.stanford.math.plex.MappedBufferData
enable(String) - Method in class bsh.PlexReader: Enable logging, making sure that there is an underlying logstream.
enableLogging() - Method in class bsh.PlexInterpreter: Turn ON input logging for this Interpreter.
enclose(Simplex[][]) - Static method in class edu.stanford.math.plex.ExplicitStream: Convert a Simplex[][] into an ExplicitStream.
end - Variable in class edu.stanford.math.plex.PersistenceBasisInterval.Float
end - Variable in class edu.stanford.math.plex.PersistenceBasisInterval.Int
end - Variable in class edu.stanford.math.plex.PersistenceInterval.Float
end - Variable in class edu.stanford.math.plex.PersistenceInterval.Int
endAllIntervals(I) - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
endInterval(K, I) - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
enqueue(Simplex) - Method in class edu.stanford.math.plex.SimplexStream.Tail
ensure_all_faces() - Method in class edu.stanford.math.plex.ExplicitStream: Make sure all of the faces of simplices in simplex_table are present in the table as well.
ensure_faces(Simplex, Double, HashMap<Simplex, Double>) - Method in class edu.stanford.math.plex.ExplicitStream
ensure_length(int[], int) - Method in class edu.stanford.math.plex.ExplicitStream
ensureAllFaces() - Method in class edu.stanford.math.plex4.streams.impl.ExplicitStream: This function ensures that all of the faces of the all of the elements are present in the stream.
entries - Variable in class edu.stanford.math.plex.SimplexStream.Stack.Segment
entry_limit - Variable in class edu.stanford.math.plex.SimplexTable
epsilon - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
epsilonNeighborhoodSearch(double[], double, boolean) - Method in class edu.stanford.math.plex4.kd.KDTree: This function finds all points within an open or closed neighborhood of the query point.
eql(SimplexStream.Head) - Method in class edu.stanford.math.plex.SimplexStream.Head: Check equality of Head with another.
equalPersistenceIntervals(PersistenceInterval.Float[], PersistenceInterval.Float[], double) - Static method in class edu.stanford.math.plex.Plex: Are two PersistenceInterval.Float[] arguments sufficiently equal?
equals(Chain) - Method in class edu.stanford.math.plex.Chain: Chain equals implementation.
equals(Object) - Method in class edu.stanford.math.plex.Packed2Simplex: Overrides Object equals.
equals(Object) - Method in class edu.stanford.math.plex.Packed4Simplex: Overrides Object equals.
equals(Object) - Method in class edu.stanford.math.plex.Packed6Simplex: Overrides Object equals.
equals(Object) - Method in class edu.stanford.math.plex.Packed8Simplex: Overrides Object equals.
equals(Object) - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Float: Are two persistence intervals equivalent.
equals(Object) - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Int: Are two persistence intervals equivalent.
equals(Object) - Method in class edu.stanford.math.plex.PersistenceInterval.Float: Are two persistence intervals equivalent.
equals(Object) - Method in class edu.stanford.math.plex.PersistenceInterval.Int: Are two persistence intervals equivalent.
equals(Object) - Method in class edu.stanford.math.plex.Plex.BettiNumbers: Determine if two instances of BettiNumbers are equal.
equals(Object) - Method in class edu.stanford.math.plex.Simplex: Overrides Object equals.
equals(Object) - Method in class edu.stanford.math.plex4.bottleneck.FlowEdge
equals(Object) - Method in class edu.stanford.math.plex4.homology.barcodes.Interval
equals(Object) - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor
equals(Object) - Method in class edu.stanford.math.plex4.homology.chain_basis.Cell
equals(Object) - Method in class edu.stanford.math.plex4.homology.chain_basis.Simplex
equals(Object) - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
equals(Object) - Method in class edu.stanford.math.plex4.visualization.Point2D
erdosGallaiCriteria(int[], int) - Static method in class edu.stanford.math.plex4.graph.random.PrescribedDegrees: Checks the Erdos-Gallai criteria for a particular value of k.
ErdosRenyiGraph - Class in edu.stanford.math.plex4.graph.random: Implements the Erdos-Renyi G(n,p) model.
ErdosRenyiGraph(int, double) - Constructor for class edu.stanford.math.plex4.graph.random.ErdosRenyiGraph
erParameter - Variable in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph
estimateDiameter(AbstractIntMetricSpace) - Static method in class edu.stanford.math.plex4.api.Plex4: This function estimates the diameter of a metric space.
estimateDiameter(AbstractIntMetricSpace, int) - Static method in class edu.stanford.math.plex4.metric.utility.MetricUtility: This function estimates the diameter of the supplied metric space.
estimateDiameter(AbstractIntMetricSpace) - Static method in class edu.stanford.math.plex4.metric.utility.MetricUtility: This function performs randomized sampling to find the estimated diameter of the given metric space.
estimateRmax(PointData, int[]) - Static method in class edu.stanford.math.plex.WitnessStream: Estimate Rmax for a given PointData and landmark set.
EuclideanArrayData - Class in edu.stanford.math.plex: The EuclideanArrayData class is the simplest implementation of NSpace.
EuclideanArrayData() - Constructor for class edu.stanford.math.plex.EuclideanArrayData
EuclideanArrayData(double[], int) - Constructor for class edu.stanford.math.plex.EuclideanArrayData: The obvious constructor for this class.
EuclideanArrayData(double[][]) - Constructor for class edu.stanford.math.plex.EuclideanArrayData: Construct a EuclideanArrayData instance from a double[][].
EuclideanArrayData(int, int) - Constructor for class edu.stanford.math.plex.EuclideanArrayData
EuclideanArrayData(int, int, double, double) - Constructor for class edu.stanford.math.plex.EuclideanArrayData
EuclideanArrayData(int, int) - Static method in class edu.stanford.math.plex.Plex: Create a random EuclideanArrayData instance.
EuclideanArrayData(double[], int) - Static method in class edu.stanford.math.plex.Plex: Create a EuclideanArrayData instance from a data array.
EuclideanArrayData(double[][]) - Static method in class edu.stanford.math.plex.Plex: Create a EuclideanArrayData instance from a double[][].
EuclideanArrayData(String) - Static method in class edu.stanford.math.plex.Plex: Create a EuclideanArrayData instance from a text file containing a distance matrix.
euclideanGcd(long, long) - Static method in class edu.stanford.math.plex4.utility.MathUtility
EuclideanMetricSpace - Class in edu.stanford.math.plex4.metric.impl: This class implements the standard metric space structure on R^n given by the Euclidean metric.
EuclideanMetricSpace(double[][]) - Constructor for class edu.stanford.math.plex4.metric.impl.EuclideanMetricSpace: This constructor initializes the class with an array of elements.
evaluate(Interval<Integer>) - Method in class edu.stanford.math.plex4.homology.filtration.FiltrationConverter
evaluate(PersistenceInterval[]) - Method in class edu.stanford.math.plex4.interop.Plex3ToPlex4BarcodeAdapter
evaluate(Simplex) - Method in class edu.stanford.math.plex4.interop.Plex3ToPlex4SimplexAdapter
evaluate(int) - Method in class edu.stanford.math.plex4.streams.filter.EccentricityFilterFunction
evaluate(int) - Method in class edu.stanford.math.plex4.streams.filter.ExplicitIntFilterFunction
evaluate(T) - Method in interface edu.stanford.math.plex4.streams.filter.FilterFunction
evaluate(int) - Method in interface edu.stanford.math.plex4.streams.filter.IntFilterFunction
evaluate(int) - Method in class edu.stanford.math.plex4.streams.filter.KernelDensityFilterFunction
evaluate(Simplex) - Method in class edu.stanford.math.plex4.streams.filter.MaxSimplicialFilterFunction
evaluate(Simplex) - Method in class edu.stanford.math.plex4.streams.filter.MinSimplicialFilterFunction
evaluate(int) - Method in class edu.stanford.math.plex4.streams.filter.RandomProjectionFilterFunction
ExceptionUtility - Class in edu.stanford.math.plex4.utility: This class contains static functions for aiding in creating exceptions, and verifying exceptions.
ExceptionUtility() - Constructor for class edu.stanford.math.plex4.utility.ExceptionUtility
explain() - Method in class edu.stanford.math.plex4.graph.random.ClusteredERGraph
ExplicitCellStream - Class in edu.stanford.math.plex4.streams.impl: This class is a wrapper for the ExplicitStream class and provides convenience functions when the base elements are cells.
ExplicitCellStream() - Constructor for class edu.stanford.math.plex4.streams.impl.ExplicitCellStream: Default constructor.
ExplicitCellStream(double) - Constructor for class edu.stanford.math.plex4.streams.impl.ExplicitCellStream
ExplicitIntFilterFunction - Class in edu.stanford.math.plex4.streams.filter
ExplicitIntFilterFunction(double[]) - Constructor for class edu.stanford.math.plex4.streams.filter.ExplicitIntFilterFunction
ExplicitLandmarkSelector<T> - Class in edu.stanford.math.plex4.metric.landmark
ExplicitLandmarkSelector(AbstractSearchableMetricSpace<T>, int[]) - Constructor for class edu.stanford.math.plex4.metric.landmark.ExplicitLandmarkSelector
ExplicitMetricSpace - Class in edu.stanford.math.plex4.metric.impl: This class implements the AbstractIntMetricSpace interface.
ExplicitMetricSpace(double[][]) - Constructor for class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace: This constructor initializes the class with the given distance matrix.
ExplicitSimplexStream - Class in edu.stanford.math.plex4.streams.impl: This class is a wrapper for the ExplicitStream class and provides convenience functions when the base elements are simplices.
ExplicitSimplexStream(Comparator<Simplex>) - Constructor for class edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream: This constructor initializes the class with the given simplex comparator.
ExplicitSimplexStream(Comparator<Simplex>, double) - Constructor for class edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream
ExplicitSimplexStream() - Constructor for class edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream: This constructor initializes the class with the default simplex comparator.
ExplicitSimplexStream(double) - Constructor for class edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream
ExplicitStream - Class in edu.stanford.math.plex: A ExplicitStream instance is SimplexStream whose elements are given explicitly, along with associated values of a persistence parameter.
ExplicitStream() - Constructor for class edu.stanford.math.plex.ExplicitStream: Constructor for ExplicitStream.
ExplicitStream() - Static method in class edu.stanford.math.plex.Plex: Make an empty ExplicitStream.
ExplicitStream<T extends PrimitiveBasisElement> - Class in edu.stanford.math.plex4.streams.impl: This class implements the functionality of a user-defined filtered chain complex.
ExplicitStream(Comparator<T>) - Constructor for class edu.stanford.math.plex4.streams.impl.ExplicitStream: Constructor which accepts a comparator for comparing the type T.
ExplicitStream(Comparator<T>, double) - Constructor for class edu.stanford.math.plex4.streams.impl.ExplicitStream
ExplicitStream(AbstractFilteredStream<T>, Comparator<T>) - Constructor for class edu.stanford.math.plex4.streams.impl.ExplicitStream: This constructor initializes the stream from an existing stream.
ExplicitStream.DComplex - Class in edu.stanford.math.plex: A DComplex (for Dimensional Complex) is the set of simplices (and associated persistence parameters) of specified dimension for an ExplicitStream.
ExplicitStream.DComplex(ExplicitStream, int, int[][], double[]) - Constructor for class edu.stanford.math.plex.ExplicitStream.DComplex: Constructor for DComplex;
ExplicitStream.ExplicitStreamIterator - Class in edu.stanford.math.plex: Instances provide Iterator for non-destructive iterating over entries.
ExplicitStream.ExplicitStreamIterator(ExplicitStream) - Constructor for class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
ExplicitStream.ExplicitStreamIterator(ExplicitStream, int) - Constructor for class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
exportScatterPlot2D(MatlabWriter, DoubleMatrix2D, String) - Static method in class edu.stanford.math.plex4.io.MatlabInterface: This function writes the commands to create a scatter plot of the data in the supplied matrix.
exportScatterPlot2D(MatlabWriter, DoubleMatrix2D, String, int[]) - Static method in class edu.stanford.math.plex4.io.MatlabInterface: This function writes the commands to create a scatter plot of the data in the supplied matrix.
exportScatterPlot3D(MatlabWriter, DoubleMatrix2D, String) - Static method in class edu.stanford.math.plex4.io.MatlabInterface: This function writes the commands to create a 3-D scatter plot of the data in the supplied matrix.
exportScatterPlot3D(MatlabWriter, DoubleMatrix2D, String, int[]) - Static method in class edu.stanford.math.plex4.io.MatlabInterface: This function writes the commands to create a 3-D scatter plot of the data in the supplied matrix.
ExternalConverter - Class in edu.stanford.math.plex4.homology.filtration: This class implements a conversion between filtration values and filtration indices that is given as an argument at instantiation of the converter.
ExternalConverter(double[]) - Constructor for class edu.stanford.math.plex4.homology.filtration.ExternalConverter
extractActiveBasisElements(ObjectSparseFormalSum<F, U>) - Static method in class edu.stanford.math.plex4.utility.FormalSumUtility: This function returns all of the basis elements in a chain which have non-zero coefficients.
extractActiveBasisElements(IntSparseFormalSum) - Static method in class edu.stanford.math.plex4.utility.FormalSumUtility: This function returns all of the basis elements in a chain which have non-zero coefficients.
extractActiveBasisElements(BooleanSparseFormalSum) - Static method in class edu.stanford.math.plex4.utility.FormalSumUtility: This function returns all of the basis elements in a chain which have non-zero coefficients.
extractCoefficients(IntSparseFormalSum<?>) - Static method in class edu.stanford.math.plex4.utility.FormalSumUtility: This function returns the coefficients for a formal sum in the form of a list.
extractCoefficients(ObjectSparseFormalSum<F, U>) - Static method in class edu.stanford.math.plex4.utility.FormalSumUtility: This function returns the coefficients for a formal sum in the form of a list.
extractVertices(List<Simplex>) - Static method in class edu.stanford.math.plex4.utility.FormalSumUtility: This function extracts the set of vertices from a list of simplices and returns a 2-d array containing the vertices.

F

F - Variable in class edu.stanford.math.plex.ExplicitStream.DComplex
F() - Method in class edu.stanford.math.plex.ExplicitStream.DComplex: Return the array of persistence parameters corresponding to the simplices of this dimension.
faces_are_consistent(Simplex, Double, boolean, boolean) - Method in class edu.stanford.math.plex.ExplicitStream
field - Variable in class edu.stanford.math.plex4.autogen.homology.IntClassicalHomology
field - Variable in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This is the field over which we perform the arithmetic computations.
field - Variable in class edu.stanford.math.plex4.autogen.homology.ObjectClassicalHomology
field - Variable in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This is the field over which we perform the arithmetic computations.
field - Variable in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This is the field over which we perform the arithmetic computations.
field - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker: This is the field over which we perform the arithmetic computations.
field - Variable in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker: This is the field over which we perform the arithmetic computations.
field - Variable in class edu.stanford.math.plex4.homology.zigzag.ZigZagHomology: This is the field over which we perform the arithmetic computations.
file_exists(String, boolean) - Static method in class edu.stanford.math.plex.MappedBufferData
FileIOUtility - Class in edu.stanford.math.plex4.io: This class contains various static functions for reading and writing files of different types.
FileIOUtility() - Constructor for class edu.stanford.math.plex4.io.FileIOUtility
FileManager - Class in edu.stanford.math.plex4.io: This class returns canonical paths so that they are in the appropriate format for the OS in use (e.g.
fileSaveMenuHandler - Variable in class edu.stanford.math.plex.BCPlot
filter(SimplexTable) - Method in class edu.stanford.math.plex.Chain: Filter simplices.
filter(List<Simplex>) - Method in class edu.stanford.math.plex.Chain
filter_pintervals(PersistenceInterval.Float[], double) - Static method in class edu.stanford.math.plex.Plex
filterByDimension(IntSparseFormalSum, int) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.SimplexStreamUtility
filterByMaxDimension(int) - Method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection
filterByMaximum(double) - Method in class edu.stanford.math.plex4.bottleneck.WeightedBipartiteGraph
filterByNeighborDistance(AbstractSearchableMetricSpace<T>, int, double) - Static method in class edu.stanford.math.plex4.metric.utility.MetricUtility
filteredComparator - Variable in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This comparator provides the dictionary ordering on filtration value - basis element pairs.
filteredComparator - Variable in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This comparator provides the dictionary ordering on filtration value - basis element pairs.
filteredComparator - Variable in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This comparator provides the dictionary ordering on filtration value - basis element pairs.
filteredComparator - Variable in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This comparator provides the dictionary ordering on filtration value - basis element pairs.
filteredComparator - Variable in class edu.stanford.math.plex4.homology.zigzag.ZigZagHomology: This comparator provides the dictionary ordering on filtration value - basis element pairs.
FilteredComparator<M> - Class in edu.stanford.math.plex4.streams.utility: This class provides filtration based comparison of basis elements.
FilteredComparator(AbstractFilteredStream<M>, Comparator<M>) - Constructor for class edu.stanford.math.plex4.streams.utility.FilteredComparator: This constructor initializes the class with a filtered chain complex, and a comparator on the basis elements.
FilteredStreamInterface - Class in edu.stanford.math.plex4.api
FilteredStreamInterface() - Constructor for class edu.stanford.math.plex4.api.FilteredStreamInterface
filterEvenIntervals(AnnotatedBarcodeCollection<Integer, G>) - Static method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection
FilterFunction<T> - Interface in edu.stanford.math.plex4.streams.filter
FilterFunctionUtility - Class in edu.stanford.math.mapper
FilterFunctionUtility() - Constructor for class edu.stanford.math.mapper.FilterFunctionUtility
FilterInfinite(PersistenceInterval[]) - Static method in class edu.stanford.math.plex.Plex: Summarize the semi-infinite PersistenceIntervals.
FilterInfinite(PersistenceBasisInterval[]) - Static method in class edu.stanford.math.plex.Plex: Summarize the semi-infinite PersistenceBasisIntervals.
filterIntervalPairsByMinimumLength(Iterable<ObjectObjectPair<Interval<Double>, G>>, double) - Static method in class edu.stanford.math.plex4.homology.barcodes.BarcodeUtility: Given a collection of intervals object pairs, this function returns those intervals with length greater than or equal to the minimum specified.
filterIntervalsByMinimumLength(Iterable<Interval<Double>>, double) - Static method in class edu.stanford.math.plex4.homology.barcodes.BarcodeUtility: Given a collection of intervals, this function returns those intervals with length greater than or equal to the minimum specified.
filterLargest(List<Interval<Double>>, int) - Static method in class edu.stanford.math.plex4.bottleneck.BottleneckDistance
filterPositiveMeasureIntervals() - Method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection
FiltrationConverter - Class in edu.stanford.math.plex4.homology.filtration: This interface defines a mapping between filtration values and filtration indices.
FiltrationConverter() - Constructor for class edu.stanford.math.plex4.homology.filtration.FiltrationConverter
FiltrationUtility - Class in edu.stanford.math.plex4.homology.filtration: This class contains various static functions that aid in the transformation between objects defined in terms of filtration indices to objects defined in terms of filtration values.
FiltrationUtility() - Constructor for class edu.stanford.math.plex4.homology.filtration.FiltrationUtility
finalizeMatlabWriter(MatlabWriter) - Static method in class edu.stanford.math.plex4.io.MatlabInterface: This function cleans up a MatlabWriter when it is no longer in use.
finalizeStream() - Method in class edu.stanford.math.plex4.interop.Plex3Stream
finalizeStream() - Method in class edu.stanford.math.plex4.streams.derived.DualStream
finalizeStream() - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
finalizeStream() - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
finalizeStream() - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
finalizeStream() - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function prepares the stream for use by a consumer, such as the PersistentHomology class.
finalizeStream() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
finalizeStream() - Method in interface edu.stanford.math.plex4.streams.multi.AbstractMultifilteredStream: This function prepares the stream for use by a consumer, such as the PersistentHomology class.
finalizeStream() - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
finalizeStructure() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
finalizeStructure() - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
finalizeStructure() - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function sets the stream as being finalized.
find(int) - Method in class edu.stanford.math.clustering.DisjointSetSystem
find(int) - Method in class edu.stanford.math.plex4.homology.nonautogen.DisjointSetSystem: Deprecated.

Returns the index of the representative
find_simplices(double, double, int, int, int[], PointData) - Method in class edu.stanford.math.plex.LazyWitnessStream
find_simplices(double, int, PointData) - Method in class edu.stanford.math.plex.RipsStream
find_simplices(double, double, int, int[], PointData) - Method in class edu.stanford.math.plex.WitnessStream
findColumnWithGivenLow(List<IntSparseFormalSum<Y>>, Y, Comparator<Y>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function finds the index of the first column such that the column's low value is the value specified.
findColumnWithGivenLow(Map<X, IntSparseFormalSum<Y>>, Y, Comparator<Y>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function finds the index of the first column such that the column's low value is the value specified.
findex - Variable in class edu.stanford.math.plex.PersistenceBasis.ListItem
findex() - Method in class edu.stanford.math.plex.Simplex: Get the findex value.
findex_bound - Variable in class edu.stanford.math.plex.SimplexStream.Stack
findexOffset - Variable in class edu.stanford.math.plex.Cone
findFirstIndexContainingElement(Map<X, IntSparseFormalSum<Y>>, Y, Comparator<X>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function returns the lowest index such that the given element is found in the chain at that index.
findLastIndexContainingElement(Map<X, IntSparseFormalSum<Y>>, Y, Comparator<X>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function returns the greatest index such that the given element is found in the chain at that index.
findPath(int, int, List<ObjectIntPair<FlowEdge>>) - Method in class edu.stanford.math.plex4.bottleneck.FlowNetwork
finite_eij_array - Variable in class edu.stanford.math.plex.LazyWitnessStream
FiniteMetricSpaceCover - Class in edu.stanford.math.mapper
FiniteMetricSpaceCover(IntFilterFunction, AbstractIntMetricSpace) - Constructor for class edu.stanford.math.mapper.FiniteMetricSpaceCover
firstSmallerPtIndex(int, int, int[]) - Static method in class edu.stanford.math.plex.Plex
fixed_dimension - Variable in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
fixed_dimension - Variable in class edu.stanford.math.plex.SimplexStream.Stack.StackIterator
FIXED_RULER_HEIGHT - Static variable in class edu.stanford.math.plex.BCPlot
fixedRuler - Variable in class edu.stanford.math.plex.BCPlot
fixedRulerBorderColor - Variable in class edu.stanford.math.plex.BCPlot
fixedRulerColor - Variable in class edu.stanford.math.plex.BCPlot
fixedRulerFont - Variable in class edu.stanford.math.plex.BCPlot
fixedRulerFontColor - Variable in class edu.stanford.math.plex.BCPlot
fixedRulerFontMetrics - Variable in class edu.stanford.math.plex.BCPlot
fixedRulerMajorTickColor - Variable in class edu.stanford.math.plex.BCPlot
fixedRulerMinorTickColor - Variable in class edu.stanford.math.plex.BCPlot
FlagComplexStream - Class in edu.stanford.math.plex4.streams.impl: This class implements a simplex stream with the property that given its 1-skeleton, its higher skeletons are maximal in the following sense.
FlagComplexStream(int, FiltrationConverter) - Constructor for class edu.stanford.math.plex4.streams.impl.FlagComplexStream: This constructor initializes the class.
FlagComplexStream(int, FiltrationConverter, int[]) - Constructor for class edu.stanford.math.plex4.streams.impl.FlagComplexStream
FlagComplexStream(int, FiltrationConverter, StreamStorageStructure<Simplex>) - Constructor for class edu.stanford.math.plex4.streams.impl.FlagComplexStream: Constructor.
FlexibleVietorisRipsStream<T> - Class in edu.stanford.math.plex4.streams.impl: This class implements the Vietoris-Rips filtered simplicial complex.
FlexibleVietorisRipsStream(AbstractSearchableMetricSpace<T>, double, int, FiltrationConverter) - Constructor for class edu.stanford.math.plex4.streams.impl.FlexibleVietorisRipsStream: Constructor which initializes the complex with a metric space.
FlexibleVietorisRipsStream(AbstractSearchableMetricSpace<T>, double, int, FiltrationConverter, StreamStorageStructure<Simplex>) - Constructor for class edu.stanford.math.plex4.streams.impl.FlexibleVietorisRipsStream
FlexibleVietorisRipsStream(AbstractSearchableMetricSpace<T>, double, int, FiltrationConverter, int[]) - Constructor for class edu.stanford.math.plex4.streams.impl.FlexibleVietorisRipsStream
floorLog2(int) - Static method in class edu.stanford.math.plex4.utility.MathUtility: This function returns the floor of the base-2 logarithm of the input.
flow - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
FlowEdge - Class in edu.stanford.math.plex4.bottleneck
FlowEdge(int, int, int) - Constructor for class edu.stanford.math.plex4.bottleneck.FlowEdge
FlowNetwork - Class in edu.stanford.math.plex4.bottleneck
FlowNetwork() - Constructor for class edu.stanford.math.plex4.bottleneck.FlowNetwork
fn(int, int) - Method in class edu.stanford.math.plex.PlexSort.Comp: Compare two int arguments, and return an integer less than, equal to, or greater than 0, depending on whether i is respectively less, equivalent, or greater than, j.
fn(long, long) - Method in class edu.stanford.math.plex.PlexSort.CompL: Compare two long arguments, and return an integer less than, equal to, or greater than 0, depending on whether i is respectively less, equivalent, or greater than, j.
fn(Object, Object) - Method in class edu.stanford.math.plex.PlexSort.CompObj: Compare two object arguments, and return an integer less than, equal to, or greater than 0, depending on whether i is respectively less, equivalent, or greater than, j.
force() - Method in class edu.stanford.math.plex.MappedBufferData: Force changes to data back to file.
FordFulkerson - Class in edu.stanford.math.plex4.bottleneck: The Ford-Fulkerson Algorithm
FordFulkerson() - Constructor for class edu.stanford.math.plex4.bottleneck.FordFulkerson
FordFulkersonEdge - Class in edu.stanford.math.plex4.bottleneck
FordFulkersonEdge(int, int, int) - Constructor for class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
FordFulkersonEdge(int, int, int, double) - Constructor for class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
FordFulkersonNode - Class in edu.stanford.math.plex4.bottleneck
FordFulkersonNode(String) - Constructor for class edu.stanford.math.plex4.bottleneck.FordFulkersonNode
ForestFireGraph - Class in edu.stanford.math.plex4.graph.random: This class creates a random graph generated from the forest fire model.
ForestFireGraph(int, double, double) - Constructor for class edu.stanford.math.plex4.graph.random.ForestFireGraph
forgetGeneratorType(AnnotatedBarcodeCollection<T, G>) - Static method in class edu.stanford.math.plex4.homology.barcodes.BarcodeCollection
FormalSumUtility - Class in edu.stanford.math.plex4.utility: This class contains various utility functions for interacting with formal sums (chains).
FormalSumUtility() - Constructor for class edu.stanford.math.plex4.utility.FormalSumUtility
forwardBurningProbability - Variable in class edu.stanford.math.plex4.graph.random.ForestFireGraph
frame - Variable in class edu.stanford.math.plex.PlexMessageWindow
fullVisualizationHeight - Variable in class edu.stanford.math.plex.BCPlot
fullVisualizationWidth - Variable in class edu.stanford.math.plex.BCPlot

G

gaussianDensity(double) - Static method in class edu.stanford.math.plex4.utility.MathUtility: This function evaluates the standard gaussian density with mean 0 and variance 1.
gaussianDensity(double, double, double) - Static method in class edu.stanford.math.plex4.utility.MathUtility: This function evaluates the 1-dimensional gaussian density function with specified mean and standard deviation.
generate() - Method in class edu.stanford.math.plex4.graph.random.BAGraph: This algorithm makes a power law graph with n nodes.
generate() - Method in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
generate() - Method in class edu.stanford.math.plex4.graph.random.BinaryTreeGraph
generate() - Method in class edu.stanford.math.plex4.graph.random.CircleGraph
generate() - Method in class edu.stanford.math.plex4.graph.random.ClusteredERGraph
generate() - Method in class edu.stanford.math.plex4.graph.random.ErdosRenyiGraph
generate() - Method in class edu.stanford.math.plex4.graph.random.ForestFireGraph
generate() - Method in class edu.stanford.math.plex4.graph.random.GraphInstanceGenerator
generate() - Method in class edu.stanford.math.plex4.graph.random.ManifoldGraph
generate() - Method in class edu.stanford.math.plex4.graph.random.PrescribedDegrees: Implements "Sequential Algorithm For Random Graph with Given Degrees" from "A SEQUENTIAL IMPORTANCE SAMPLING ALGORITHM FOR GENERATING RANDOM GRAPHS WITH PRESCRIBED DEGREES" By Joseph Blitzstein and Persi Diaconis
generate() - Method in class edu.stanford.math.plex4.graph.random.RandomGeometricGraph
generate() - Method in class edu.stanford.math.plex4.graph.random.StochasticBlockmodel
generatePoints() - Method in class edu.stanford.math.plex4.graph.random.KNearestNeighborsGraph
generatePoints() - Method in class edu.stanford.math.plex4.graph.random.ManifoldGraph: This function must generate the set of random points on the manifold.
generatePoints() - Method in class edu.stanford.math.plex4.graph.random.SphereGraph
generatePoints() - Method in class edu.stanford.math.plex4.graph.random.TorusGraph
generateString(int) - Method in class edu.stanford.math.mapper.HistogramCreator
generateUniformPoints() - Method in class edu.stanford.math.plex4.graph.random.ManifoldGraph: This function generates points on the d-dimensional cube [0, 1]^d.
generateUniqueFileName() - Static method in class edu.stanford.math.plex4.io.FileManager: This function creates a unique filename.
generateWithRewiring(AbstractUndirectedGraph) - Method in class edu.stanford.math.plex4.graph.random.CircleGraph
generator - Variable in class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
GeneratorDriver - Class in edu.stanford.math.plex4.generation: This class contains functions for creating auto-generated code.
GeneratorDriver() - Constructor for class edu.stanford.math.plex4.generation.GeneratorDriver
generators - Variable in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor
GeometricSimplexStream - Class in edu.stanford.math.plex4.streams.impl: This class defines a geometric realization of a filtered simplicial complex, ie.
GeometricSimplexStream(AbstractFilteredStream<Simplex>, AbstractObjectMetricSpace<double[]>) - Constructor for class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream: This constructor initializes the geometric complex from an abstract filtered complex and a metric space.
GeometricSimplexStream(AbstractFilteredStream<Simplex>, double[][]) - Constructor for class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream: This constructor initializes the geometric complex from an abstract simplicial complex and double array whose rows consist of the Euclidean coordinates of the vertices.
get(Simplex) - Method in class edu.stanford.math.plex.SimplexTable: Get the interned version of the Simplex s.
get_pt(int, double[]) - Method in class edu.stanford.math.plex.EuclideanArrayData: Get point.
get_pt(int, double[]) - Method in class edu.stanford.math.plex.MappedBufferData: Get point.
getAbsoluteCohomologyBarcodes() - Method in class edu.stanford.math.plex4.examples.DeSilvaMorozovJohanssonExample: This function returns the correct absolute cohomology barcodes along with the generators.
getAbsoluteHomologyBarcodes() - Method in class edu.stanford.math.plex4.examples.DeSilvaMorozovJohanssonExample: This function returns the correct absolute homology barcodes along with the generators.
getActiveGenerators() - Method in interface edu.stanford.math.plex4.homology.zigzag.AbstractPersistenceTracker
getActiveGenerators() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
getAdjacencyMatrix(AbstractUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility: This function computes the adjacency matrix of the given graph.
getAdjacencyMatrix(AbstractWeightedUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility: This function computes the adjacency matrix of the given graph.
getAllCellularAbsoluteHomologyAlgorithms(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getAllDistances(AbstractIntMetricSpace, int) - Static method in class edu.stanford.math.plex4.metric.utility.MetricUtility
getAllPlex4SimplicialAbsoluteHomologyAlgorithms(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getAllSimplexPairAbsoluteHomologyAlgorithms(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getAllSimplicialAbsoluteHomologyAlgorithms(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getAllWitnesses(double, int...) - Method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
getAnnotatedBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
getAnnotatedBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
getAnnotatedBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, BooleanSparseFormalSum>, THashMap<U, BooleanSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanAbsoluteHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, BooleanSparseFormalSum>, THashMap<U, BooleanSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistentHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, BooleanSparseFormalSum>, THashMap<U, BooleanSparseFormalSum>>, AbstractFilteredStream, boolean) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistentHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, BooleanSparseFormalSum>, THashMap<U, BooleanSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanRelativeHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, IntSparseFormalSum>, THashMap<U, IntSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntAbsoluteHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, IntSparseFormalSum>, THashMap<U, IntSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistentHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, IntSparseFormalSum>, THashMap<U, IntSparseFormalSum>>, AbstractFilteredStream, boolean) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistentHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, IntSparseFormalSum>, THashMap<U, IntSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntRelativeHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, ObjectSparseFormalSum<F, U>>, THashMap<U, ObjectSparseFormalSum<F, U>>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectAbsoluteHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, ObjectSparseFormalSum<F, U>>, THashMap<U, ObjectSparseFormalSum<F, U>>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistentHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, ObjectSparseFormalSum<F, U>>, THashMap<U, ObjectSparseFormalSum<F, U>>>, AbstractFilteredStream, boolean) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistentHomology
getAnnotatedIntervals(ObjectObjectPair<THashMap<U, ObjectSparseFormalSum<F, U>>, THashMap<U, ObjectSparseFormalSum<F, U>>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectRelativeHomology
getAnnulus(int, int) - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples
getAnnulusVertices(int, int) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples
getAppendIndex(Map<Integer, X>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
getAscendingIndices(Map<X, Y>, Comparator<X>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
getAscendingIndicesContainingElement(Map<X, IntSparseFormalSum<Y>>, Y, Comparator<X>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function returns the set of indices such that the chains at the indices contain the given element.
getAscendingIndicesWithGivenLow(Map<X, IntSparseFormalSum<Y>>, Y, Comparator<X>, Comparator<Y>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
getAssociatedSimplices(int) - Method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream: This function returns the list of simplices such that they have the given point as their witness.
getAssociatedSimplices(int) - Method in class edu.stanford.math.plex4.streams.impl.WitnessStream: This function returns the list of simplices such that they have the given point as their witness.
getBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
getBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
getBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
getBaseOutputPath() - Static method in class edu.stanford.math.plex4.io.FileManager: This function returns the base output path.
getBasisComparator() - Method in class edu.stanford.math.plex4.interop.Plex3Stream
getBasisComparator() - Method in class edu.stanford.math.plex4.streams.derived.DualStream
getBasisComparator() - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
getBasisComparator() - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
getBasisComparator() - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getBasisComparator() - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function returns a comparator on the underlying basis type.
getBasisComparator() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
getBasisComparator() - Method in interface edu.stanford.math.plex4.streams.multi.AbstractMultifilteredStream: This function returns a comparator on the underlying basis type.
getBasisComparator() - Method in class edu.stanford.math.plex4.streams.multi.BifilteredMetricStream
getBasisComparator() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
getBasisComparator() - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
getBasisComparator() - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function returns a Comparator object used to define the ordering on the basis type.
getBettiNumbers() - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function returns a string representation of the set of betti numbers.
getBettiNumbersMap(T) - Method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection
getBettiSequence() - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function returns an array of integers indicating the cardinality of the barcodes at each dimension.
getBinEndingPoints() - Method in class edu.stanford.math.mapper.HistogramCreator
getBinLattice(double) - Method in class edu.stanford.math.mapper.HistogramCreator
getBinLatticePoint(int, double) - Method in class edu.stanford.math.mapper.HistogramCreator
getBinMidPoints() - Method in class edu.stanford.math.mapper.HistogramCreator
getBinStartingPoints() - Method in class edu.stanford.math.mapper.HistogramCreator
getBinStartPoint(int) - Method in class edu.stanford.math.mapper.HistogramCreator
getBooleanCellularAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getBooleanCellularClassicalHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getBooleanCellularRelativeHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getBooleanSimplexPairAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getBooleanSimplexPairClassicalHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getBooleanSimplexPairRelativeHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getBooleanSimplicialAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getBooleanSimplicialClassicalHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getBooleanSimplicialRelativeHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getBoundary(Simplex) - Method in class edu.stanford.math.plex4.interop.Plex3Stream
getBoundary(T) - Method in class edu.stanford.math.plex4.streams.derived.DualStream
getBoundary(ObjectObjectPair<T, U>) - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
getBoundary(T) - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
getBoundary(Simplex) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getBoundary(T) - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function returns the elements in the boundary of the supplied basisElement, without the coefficients.
getBoundary(T) - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
getBoundary(T) - Method in interface edu.stanford.math.plex4.streams.multi.AbstractMultifilteredStream: This function returns the elements in the boundary of the supplied basisElement, without the coefficients.
getBoundary(T) - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
getBoundaryArray() - Method in class edu.stanford.math.plex4.homology.chain_basis.Cell
getBoundaryArray() - Method in interface edu.stanford.math.plex4.homology.chain_basis.PrimitiveBasisElement: This function returns the boundary of the current basis element.
getBoundaryArray() - Method in class edu.stanford.math.plex4.homology.chain_basis.Simplex
getBoundaryArray() - Method in class edu.stanford.math.plex4.homology.chain_basis.SimplexPair
getBoundaryCoefficients() - Method in class edu.stanford.math.plex4.homology.chain_basis.Cell
getBoundaryCoefficients() - Method in interface edu.stanford.math.plex4.homology.chain_basis.PrimitiveBasisElement: This function returns the coefficients of the elements of the boundary array.
getBoundaryCoefficients() - Method in class edu.stanford.math.plex4.homology.chain_basis.Simplex
getBoundaryCoefficients() - Method in class edu.stanford.math.plex4.homology.chain_basis.SimplexPair
getBoundaryCoefficients(Simplex) - Method in class edu.stanford.math.plex4.interop.Plex3Stream
getBoundaryCoefficients(T) - Method in class edu.stanford.math.plex4.streams.derived.DualStream
getBoundaryCoefficients(ObjectObjectPair<T, U>) - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
getBoundaryCoefficients(T) - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
getBoundaryCoefficients(Simplex) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getBoundaryCoefficients(T) - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function returns the coefficients of the boundary of the supplied basis element.
getBoundaryCoefficients(T) - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
getBoundaryCoefficients(T) - Method in interface edu.stanford.math.plex4.streams.multi.AbstractMultifilteredStream: This function returns the coefficients of the boundary of the supplied basis element.
getBoundaryCoefficients(T) - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
getBoundaryIds() - Method in class edu.stanford.math.plex4.homology.chain_basis.Cell: This function returns the cell ids of the boundary elements.
getBoundaryMatrixColumns(AbstractFilteredStream<T>, int) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function returns the boundary matrix at the specified dimension as a list of columns
getBoundaryMatrixColumns(AbstractFilteredStream<T>, int, ObjectAlgebraicFreeModule<R, T>) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function produces a list of formal sums which are the columns of the boundary matrix at the requested dimension.
getCandidateList(int[], int, AbstractUndirectedGraph) - Method in class edu.stanford.math.plex4.graph.random.PrescribedDegrees: Computes the set of j!=i such that multiminus(d,i,j) is graphical and (i,j) is not already an edge.
getCapacity() - Method in class edu.stanford.math.plex4.bottleneck.FlowEdge
getCategoryOutputPath(String) - Static method in class edu.stanford.math.plex4.io.FileManager: This function returns the category output path.
getCellComplex() - Method in class edu.stanford.math.plex4.examples.DeSilvaMorozovJohanssonExample: This function returns the cell complex.
getCellId() - Method in class edu.stanford.math.plex4.homology.chain_basis.Cell: This function returns the unique identifier of the cell.
getCellularKleinBottle() - Static method in class edu.stanford.math.plex4.examples.CellStreamExamples: This function returns a cellular Klein bottle.
getCellularMobiusBand() - Static method in class edu.stanford.math.plex4.examples.CellStreamExamples: This function returns a cell decomposition of the Mobius band.
getCellularRP2() - Static method in class edu.stanford.math.plex4.examples.CellStreamExamples: This function returns a cell decomposition of RP^2 (the real projective plane).
getCellularSphere(int) - Static method in class edu.stanford.math.plex4.examples.CellStreamExamples: This function returns a cell decomposition of the n-sphere.
getCellularTorus() - Static method in class edu.stanford.math.plex4.examples.CellStreamExamples: This function returns a static cell complex containing a torus.
getChainModule() - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This function returns the free module used for the arithmetic computations.
getChainModule() - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This function returns the free module used for the arithmetic computations.
getChainModule() - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This function returns the free module used for the arithmetic computations.
getChainModule() - Method in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This function returns the free module used for the arithmetic computations.
getCircle(int) - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function returns a simplicial circle with m vertices in it.
getClosedNeighborhood(double[], double) - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
getClosedNeighborhood(Integer, double) - Method in class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace
getClosedNeighborhood(T, double) - Method in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace
getClosedNeighborhood(T, double) - Method in interface edu.stanford.math.plex4.metric.interfaces.AbstractSearchableMetricSpace: This function returns the set of indices of points that are contained in the closed ball of radius epsilon, centered at the specified query point.
getClosedNeighborhood(T, double) - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
getColorCode(int) - Method in class edu.stanford.math.plex4.io.MatlabWriter
getColumnHeading(int) - Method in class edu.stanford.math.plex4.io.Table: This function returns the heading of the specified column.
getCommonAncestor(int, int) - Method in class edu.stanford.math.plex4.graph.random.BinaryTree
getConverter() - Method in class edu.stanford.math.plex4.streams.impl.FlagComplexStream: This function returns the FiltrationConverter object used by the complex.
getCounts() - Method in class edu.stanford.math.mapper.HistogramCreator
getDailyOutputPath() - Static method in class edu.stanford.math.plex4.io.FileManager: This function returns the daily output path.
getDefaultBoundaryCoefficients(int) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility: This function returns the standard sequence of boundary coefficients used in simplicial homology, defined by c_i = (-1)^i.
getDefaultCellularAlgorithm(int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function returns the default (absolute) cellular persistent homology algorithm.
getDefaultEncoderFormat() - Static method in class edu.stanford.math.plex4.io.BufferedImageWriter
getDefaultExtension() - Static method in class edu.stanford.math.plex4.io.MatlabInterface
getDefaultNuValue() - Static method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
getDefaultSimplicialAlgorithm(int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function returns the default (absolute) simplicial persistent homology algorithm.
getDefaultSimplicialPairAlgorithm(int) - Static method in class edu.stanford.math.plex4.api.Plex4
getDefaultStorageStructure(Comparator<T>) - Static method in class edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructureFactory: This function returns the default stream storage structure for the type T.
getDegree(int) - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph
getDegree(int) - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph
getDegree(int) - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
getDegreeSequence() - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph
getDegreeSequence() - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph
getDegreeSequence() - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
getDelta() - Method in class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter
getDepth(int) - Method in class edu.stanford.math.plex4.graph.random.BinaryTree: Returns the depth of a node in a breadth-first labeled binary tree rooted at 1.
getDest() - Method in class edu.stanford.math.plex4.bottleneck.FlowEdge
getDiameter(DoubleSparseFormalSum<Simplex>) - Method in class edu.stanford.math.plex4.streams.utility.SkeletalMetric
getDifference(Iterable, Iterable) - Static method in class edu.stanford.math.plex4.utility.CollectionUtility
getDimension() - Method in class edu.stanford.math.plex.SimplexFaceIterator: Return the dimension of the faces generated by this iterator.
getDimension() - Method in class edu.stanford.math.plex4.homology.chain_basis.Cell
getDimension() - Method in interface edu.stanford.math.plex4.homology.chain_basis.PrimitiveBasisElement: This function returns the dimension of the basis element.
getDimension() - Method in class edu.stanford.math.plex4.homology.chain_basis.Simplex
getDimension() - Method in class edu.stanford.math.plex4.homology.chain_basis.SimplexPair
getDimension() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
getDimension(Simplex) - Method in class edu.stanford.math.plex4.interop.Plex3Stream
getDimension(T) - Method in class edu.stanford.math.plex4.streams.derived.DualStream
getDimension(ObjectObjectPair<T, U>) - Method in class edu.stanford.math.plex4.streams.derived.HomStream
getDimension(ObjectObjectPair<T, U>) - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
getDimension(T) - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
getDimension(Simplex) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getDimension(T) - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function returns the dimension of a basis element within the chain complex.
getDimension(T) - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
getDimension(T) - Method in interface edu.stanford.math.plex4.streams.multi.AbstractMultifilteredStream: This function returns the dimension of a basis element within the chain complex.
getDimension(T) - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
getDimensions() - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function returns the set of dimensions at which there are intervals.
getDisjointPatches(int) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples
getEdges(int) - Method in class edu.stanford.math.plex4.bottleneck.FlowNetwork
getEnd() - Method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns the end of the interval.
getEndpoints(AnnotatedBarcodeCollection<Double, G>, int, boolean) - Static method in class edu.stanford.math.plex4.homology.barcodes.BarcodeUtility: This function returns an array containing the set of endpoint of the intervals.
getEndpoints(List<Interval<Double>>, int, boolean) - Static method in class edu.stanford.math.plex4.homology.barcodes.BarcodeUtility: This function returns an array containing the set of endpoint of the intervals.
getEntry(int, int) - Method in class edu.stanford.math.plex4.io.Table: This function returns the entry in the table located at (row, column).
getEquispacedCirclePoints(int) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function returns a point set containing n equally spaced points on a circle.
getERHierarchyLevelCount(int) - Method in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph
getErParameter() - Method in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph
getExtension() - Method in class edu.stanford.math.plex4.graph.io.GraphDotWriter
getExtension() - Method in class edu.stanford.math.plex4.io.BarcodeWriter
getExtension() - Method in class edu.stanford.math.plex4.io.BufferedImageWriter
getExtension() - Method in class edu.stanford.math.plex4.io.DoubleArrayReaderWriter
getExtension() - Method in interface edu.stanford.math.plex4.io.ObjectWriter
getExtension() - Method in class edu.stanford.math.plex4.io.SimplexStreamReaderWriter
getField() - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This function returns the field over which the homology is computed.
getField() - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This function returns the field over which the homology is computed.
getField() - Method in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This function returns the field over which the homology is computed.
getFilteredTriangle() - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function returns a filtered triangle where each simplex enters at a new filtration index.
getFiltrationIndex(double) - Method in class edu.stanford.math.plex4.homology.filtration.ExternalConverter: This function computes the index based on a filtration value.
getFiltrationIndex(double) - Method in class edu.stanford.math.plex4.homology.filtration.FiltrationConverter: This function computes the index based on a filtration value.
getFiltrationIndex(double) - Method in class edu.stanford.math.plex4.homology.filtration.IdentityConverter
getFiltrationIndex(double) - Method in class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter
getFiltrationIndex(double) - Method in class edu.stanford.math.plex4.homology.filtration.StaticConverter
getFiltrationIndex(Simplex) - Method in class edu.stanford.math.plex4.interop.Plex3Stream
getFiltrationIndex(T) - Method in class edu.stanford.math.plex4.streams.derived.DualStream
getFiltrationIndex(ObjectObjectPair<T, U>) - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
getFiltrationIndex(T) - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
getFiltrationIndex(Simplex) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getFiltrationIndex(T) - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function returns the filtration index of the requested basis element.
getFiltrationIndex(T) - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
getFiltrationIndex(T) - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
getFiltrationIndex(T) - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
getFiltrationIndex(T) - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function returns the filtration index of the given basis element.
getFiltrationValue(int) - Method in class edu.stanford.math.plex4.homology.filtration.ExternalConverter: This function computes the filtration value from a filtration index.
getFiltrationValue(int) - Method in class edu.stanford.math.plex4.homology.filtration.FiltrationConverter: This function computes the filtration value from a filtration index.
getFiltrationValue(int) - Method in class edu.stanford.math.plex4.homology.filtration.IdentityConverter
getFiltrationValue(int) - Method in class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter
getFiltrationValue(int) - Method in class edu.stanford.math.plex4.homology.filtration.StaticConverter
getFiltrationValue(Simplex) - Method in class edu.stanford.math.plex4.interop.Plex3Stream
getFiltrationValue(T) - Method in class edu.stanford.math.plex4.streams.derived.DualStream
getFiltrationValue(ObjectObjectPair<T, U>) - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
getFiltrationValue(T) - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
getFiltrationValue(T) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitStream
getFiltrationValue(Simplex) - Method in class edu.stanford.math.plex4.streams.impl.FlagComplexStream
getFiltrationValue(Simplex) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getFiltrationValue(Simplex) - Method in class edu.stanford.math.plex4.streams.impl.WitnessStream
getFiltrationValue(T) - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream
getFiltrationValue(T) - Method in interface edu.stanford.math.plex4.streams.multi.AbstractMultifilteredStream: This function returns the filtration multi-index of the requested basis element.
getFiltrationValue(T) - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
getFiniteAnnotatedBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
getFiniteAnnotatedBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
getFiniteAnnotatedBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
getFiniteBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
getFiniteBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
getFiniteBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
getFirstGradedProjectionMap(IntAlgebraicFreeModule, IntAlgebraicFreeModule<V>) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.InducedHomologyMappingUtility
getFlow(FlowEdge) - Method in class edu.stanford.math.plex4.bottleneck.FlowNetwork
getFormats() - Method in class edu.stanford.math.plex.BCPlot
getGaussianPoints(int, int) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function returns n points distributed to a standard Gaussian distribution in d-dimensional Euclidean space.
getGenerator() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
getGeneratorIterator() - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function returns an iterator for traversing the generators.
getGeneratorsAtDimension(int) - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function returns the set of generators at a specified dimension.
getHashedStorageStructure(Comparator<T>) - Static method in class edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructureFactory: This function creates a new hashed storage structure.
getHgLeafCount() - Method in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph
getHomotopies() - Method in class edu.stanford.math.plex4.streams.derived.HomStream
getHomotopies(ObjectAlgebraicFreeModule<R, ObjectObjectPair<T, U>>) - Method in class edu.stanford.math.plex4.streams.derived.HomStream: This function returns the set of chain homotopies of between the domain and codomain chain complexes.
getHomotopiesAsDouble(ObjectAlgebraicFreeModule<R, ObjectObjectPair<T, U>>) - Method in class edu.stanford.math.plex4.streams.derived.HomStream: This function returns the set of chain homotopies between the domain and codomain chain complexes as formal sums over pairs with double coefficients.
getHouseExample() - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This produces the house example in the tutorial by Henry Adams.
getIcosahedron() - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples
getIcosahedronVertices() - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples
getImpliedClusters(DisjointSetSystem) - Static method in class edu.stanford.math.clustering.HierarchicalClustering
getImpliedClustersTrove(DisjointSetSystem) - Static method in class edu.stanford.math.clustering.HierarchicalClustering
getInactiveGenerators() - Method in interface edu.stanford.math.plex4.homology.zigzag.AbstractPersistenceTracker
getInactiveGenerators() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
getInclusionMap() - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.InducedHomologyMappingUtility
getIndex() - Method in class edu.stanford.math.plex4.kd.KDNode
getIndices() - Method in class edu.stanford.math.plex4.metric.impl.TruncatedPriorityQueue: This function returns the list of indices currently in the queue.
getInfiniteAnnotatedBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
getInfiniteAnnotatedBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
getInfiniteAnnotatedBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
getInfiniteBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
getInfiniteBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
getInfiniteBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
getInfiniteIntervals() - Method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection
getInitialFiltrationValue() - Method in class edu.stanford.math.plex4.homology.filtration.ExternalConverter: This function returns the filtration at index 0.
getInitialFiltrationValue() - Method in class edu.stanford.math.plex4.homology.filtration.FiltrationConverter: This function returns the filtration at index 0.
getInitialFiltrationValue() - Method in class edu.stanford.math.plex4.homology.filtration.IdentityConverter
getInitialFiltrationValue() - Method in class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter
getInitialFiltrationValue() - Method in class edu.stanford.math.plex4.homology.filtration.StaticConverter
getInstance() - Static method in class edu.stanford.math.plex4.graph.metric.ShortestPathMetric
getInstance() - Static method in class edu.stanford.math.plex4.homology.barcodes.IntervalLengthComparator
getInstance() - Static method in class edu.stanford.math.plex4.homology.chain_basis.CellComparator: This static function returns the one instance of the class.
getInstance() - Static method in class edu.stanford.math.plex4.homology.chain_basis.SimplexComparator: This static function returns the one instance of the class.
getInstance() - Static method in class edu.stanford.math.plex4.homology.chain_basis.SimplexPairComparator: This static function returns the one instance of the class.
getInstance() - Static method in class edu.stanford.math.plex4.homology.filtration.IdentityConverter: This returns the single instance of the class.
getInstance() - Static method in class edu.stanford.math.plex4.homology.filtration.StaticConverter: This returns the single instance of the class.
getInstance() - Static method in class edu.stanford.math.plex4.interop.Plex3ToPlex4BarcodeAdapter
getInstance() - Static method in class edu.stanford.math.plex4.interop.Plex3ToPlex4SimplexAdapter
getInstance(int[]) - Static method in class edu.stanford.math.plex4.interop.Plex3ToPlex4SimplexAdapter
getInstance() - Static method in class edu.stanford.math.plex4.io.BarcodeWriter
getInstance(String) - Static method in class edu.stanford.math.plex4.io.BufferedImageWriter
getInstance() - Static method in class edu.stanford.math.plex4.io.DoubleArrayReaderWriter
getInstance() - Static method in class edu.stanford.math.plex4.io.SimplexStreamReaderWriter
getIntCellularAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getIntCellularClassicalHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getIntCellularRelativeHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getInterned(Simplex) - Method in class edu.stanford.math.plex.SimplexTable: Return the interned version of a Simplex.
getIntervalGeneratorPairIterator() - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function returns an iterator for traversing the interval-generator pairs.
getIntervalGeneratorPairsAtDimension(int) - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function returns the set of interval-generator pairs at a specified dimension.
getIntervalIterator() - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function returns an iterator for traversing the intervals.
getIntervals(ObjectObjectPair<THashMap<U, BooleanSparseFormalSum>, THashMap<U, BooleanSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanAbsoluteHomology
getIntervals(ObjectObjectPair<THashMap<U, BooleanSparseFormalSum>, THashMap<U, BooleanSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistentHomology
getIntervals(ObjectObjectPair<THashMap<U, BooleanSparseFormalSum>, THashMap<U, BooleanSparseFormalSum>>, AbstractFilteredStream, boolean) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistentHomology
getIntervals(ObjectObjectPair<THashMap<U, BooleanSparseFormalSum>, THashMap<U, BooleanSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanRelativeHomology
getIntervals(ObjectObjectPair<THashMap<U, IntSparseFormalSum>, THashMap<U, IntSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntAbsoluteHomology
getIntervals(ObjectObjectPair<THashMap<U, IntSparseFormalSum>, THashMap<U, IntSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistentHomology
getIntervals(ObjectObjectPair<THashMap<U, IntSparseFormalSum>, THashMap<U, IntSparseFormalSum>>, AbstractFilteredStream, boolean) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistentHomology
getIntervals(ObjectObjectPair<THashMap<U, IntSparseFormalSum>, THashMap<U, IntSparseFormalSum>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntRelativeHomology
getIntervals(ObjectObjectPair<THashMap<U, ObjectSparseFormalSum<F, U>>, THashMap<U, ObjectSparseFormalSum<F, U>>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectAbsoluteHomology
getIntervals(ObjectObjectPair<THashMap<U, ObjectSparseFormalSum<F, U>>, THashMap<U, ObjectSparseFormalSum<F, U>>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistentHomology
getIntervals(ObjectObjectPair<THashMap<U, ObjectSparseFormalSum<F, U>>, THashMap<U, ObjectSparseFormalSum<F, U>>>, AbstractFilteredStream, boolean) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistentHomology
getIntervals(ObjectObjectPair<THashMap<U, ObjectSparseFormalSum<F, U>>, THashMap<U, ObjectSparseFormalSum<F, U>>>, AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectRelativeHomology
getIntervalsAtDimension(int) - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function returns the set of intervals at a specified dimension.
getIntervalTracker() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
getIntervalTracker() - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
getIntSimplexPairAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getIntSimplexPairClassicalHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getIntSimplexPairRelativeHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getIntSimplicialAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getIntSimplicialClassicalHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getIntSimplicialRelativeHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getKNearestNeighbors(Integer, int) - Method in class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace
getKNearestNeighbors(T, int) - Method in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace
getKNearestNeighbors(T, int) - Method in interface edu.stanford.math.plex4.metric.interfaces.AbstractSearchableMetricSpace: This function returns the indices of the k points that are closest to the given query point.
getKNearestNeighbors(T, int) - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
getKthNearestNeighborDistances(AbstractSearchableMetricSpace<T>, int) - Static method in class edu.stanford.math.plex4.metric.utility.MetricUtility
getLandmarkIndex(int) - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector: This function returns the index of the i-th landmark point.
getLandmarkPoints() - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
getLandmarkSelector(int) - Method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
getLaplacianMatrix(AbstractUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility: This function computes the Laplacian matrix of a graph.
getLaplacianMatrix(AbstractWeightedUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility: This function computes the Laplacian matrix of a graph.
getLastZeroBinIndex() - Method in class edu.stanford.math.mapper.HistogramCreator
getLeft() - Method in class edu.stanford.math.plex4.kd.KDNode
getLength(Interval<Double>) - Static method in class edu.stanford.math.plex4.homology.barcodes.BarcodeUtility
getLineStyle(int) - Method in class edu.stanford.math.plex4.io.MatlabWriter
getListOfPairs() - Method in class edu.stanford.math.plex4.metric.impl.TruncatedPriorityQueue: This function returns the list of object-value pairs currently in the queue.
getLongestAnnotatedBarcodes(List<ObjectObjectPair<Interval<Double>, G>>, int) - Static method in class edu.stanford.math.plex4.homology.barcodes.BarcodeUtility
getLongestBarcodes(List<Interval<Double>>, int) - Static method in class edu.stanford.math.plex4.homology.barcodes.BarcodeUtility
getLowerNeighbors(int) - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph: This function returns the set of neighbors of vertex i in the graph which have indices less than i.
getLowerNeighbors(int) - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph: This function returns the set of neighbors of vertex i in the graph which have indices less than i.
getLowerNeighbors(int) - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph: This function returns the set of neighbors of vertex i in the graph which have indices less than i.
getMarkerStyle(int) - Method in class edu.stanford.math.plex4.io.MatlabWriter
getMax() - Method in class edu.stanford.math.mapper.HistogramCreator
getMaxBarWidth(List<Interval<Double>>) - Static method in class edu.stanford.math.plex4.visualization.BarcodeVisualizer
getMaxDepth() - Method in class edu.stanford.math.plex4.graph.random.BinaryTree
getMaxDisplayableBars() - Method in class edu.stanford.math.plex.BCPlot: Returns the maximum number of barcodes that can be "plotted".
getMaxDistanceFromPointsToLandmarks() - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector: This function returns the maximum distance between points in the landmark selection and points not in the selection.
getMaxFiltrationValue() - Method in class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter
getMaximumCoordinates() - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
getMaximumFiltrationIndex() - Method in class edu.stanford.math.plex4.interop.Plex3Stream
getMaximumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.derived.DualStream
getMaximumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
getMaximumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
getMaximumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getMaximumFiltrationIndex() - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function gets the maximum filtration index in the complex.
getMaximumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
getMaximumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
getMaximumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
getMaximumFiltrationIndex() - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function gets the maximum filtration index in the complex.
getMaxValue() - Method in class edu.stanford.math.plex4.streams.filter.EccentricityFilterFunction
getMaxValue() - Method in class edu.stanford.math.plex4.streams.filter.ExplicitIntFilterFunction
getMaxValue() - Method in interface edu.stanford.math.plex4.streams.filter.IntFilterFunction
getMaxValue() - Method in class edu.stanford.math.plex4.streams.filter.KernelDensityFilterFunction
getMaxValue() - Method in class edu.stanford.math.plex4.streams.filter.RandomProjectionFilterFunction
getMergedDistances() - Method in class edu.stanford.math.clustering.HierarchicalClustering
getMin() - Method in class edu.stanford.math.mapper.HistogramCreator
getMinFiltrationValue() - Method in class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter
getMinimumCoordinates() - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
getMinimumFiltrationIndex() - Method in class edu.stanford.math.plex4.interop.Plex3Stream
getMinimumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.derived.DualStream
getMinimumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
getMinimumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
getMinimumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getMinimumFiltrationIndex() - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function gets the minimum filtration index in the complex.
getMinimumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
getMinimumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
getMinimumFiltrationIndex() - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
getMinimumFiltrationIndex() - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function gets the minimum filtration index in the complex.
getMinValue() - Method in class edu.stanford.math.plex4.streams.filter.EccentricityFilterFunction
getMinValue() - Method in class edu.stanford.math.plex4.streams.filter.ExplicitIntFilterFunction
getMinValue() - Method in interface edu.stanford.math.plex4.streams.filter.IntFilterFunction
getMinValue() - Method in class edu.stanford.math.plex4.streams.filter.KernelDensityFilterFunction
getMinValue() - Method in class edu.stanford.math.plex4.streams.filter.RandomProjectionFilterFunction
getModularCellularAlgorithm(int, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function returns a cellular persistence algorithm over the finite field Z/pZ.
getModularSimplicialAlgorithm(int, int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function returns a simplicial persistence algorithm over the finite field Z/pZ.
getMorozovJohanssonExample() - Static method in class edu.stanford.math.plex4.examples.CellStreamExamples: This function returns the filtered cell complex which is the running example in the paper "Dualities in Persistent (Co)homology" by de Silva, Morozov and Johansson.
getNearestNeighbors(int) - Method in class edu.stanford.math.plex4.graph.random.ManifoldGraph: This function gets the indices of the k nearest neighbors to the point at the specified index.
getNearestPointIndex(double[]) - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
getNearestPointIndex(Integer) - Method in class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace
getNearestPointIndex(T) - Method in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace
getNearestPointIndex(T) - Method in interface edu.stanford.math.plex4.metric.interfaces.AbstractSearchableMetricSpace: This function returns the index of the point within the metric space nearest to the given query point.
getNearestPointIndex(T) - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
getNeighborhoodGraph() - Method in class edu.stanford.math.plex4.streams.impl.FlagComplexStream: This returns the neighborhood graph (equivalent to the 1-skeleton) of the complex.
getNeighborhoodGraph(AbstractFilteredStream<Simplex>, int) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function returns a graph containing the 1-skeleton of a given filtered simplicial complex.
getNeighborhoodGraph(AbstractFilteredStream<Simplex>) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function returns the 1-skeleton of a filtered simplicial complex in the form of an undirected graph.
getNeighbors(int) - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph
getNeighbors(int) - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph
getNeighbors(int) - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
getNextColor() - Method in class edu.stanford.math.plex4.io.MatlabWriter
getNextLineStyle() - Method in class edu.stanford.math.plex4.io.MatlabWriter
getNextMarker() - Method in class edu.stanford.math.plex4.io.MatlabWriter
getNumDivisions() - Method in class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter
getNumEdges() - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph: Gets the number of edges in the graph.
getNumEdges() - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph
getNumEdges() - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
getNumVertices() - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph: Gets the number of vertices in the graph.
getNumVertices() - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph
getNumVertices() - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
getOctahedron() - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function returns a simplicial octahedron.
getOctahedronVertices() - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function returns the vertices of an octahedron.
getOpenNeighborhood(double[], double) - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
getOpenNeighborhood(Integer, double) - Method in class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace
getOpenNeighborhood(T, double) - Method in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace
getOpenNeighborhood(T, double) - Method in interface edu.stanford.math.plex4.metric.interfaces.AbstractSearchableMetricSpace: This function returns the set of indices of points that are contained in the open ball of radius epsilon, centered at the specified query point.
getOpenNeighborhood(T, double) - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
getPlex3SimplicialAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getPoint(int) - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
getPoint(int) - Method in class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace
getPoint(int) - Method in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace
getPoint(int) - Method in interface edu.stanford.math.plex4.metric.interfaces.AbstractObjectMetricSpace: This function returns the point at the specified index.
getPoint(int) - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
getPoint(int) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getPoint(int) - Method in class edu.stanford.math.plex4.streams.utility.SkeletalMetric
getPoints() - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
getPoints() - Method in class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace
getPoints() - Method in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace
getPoints() - Method in interface edu.stanford.math.plex4.metric.interfaces.AbstractObjectMetricSpace: This function returns the set of points in the metric space as an array.
getPoints() - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
getPoints() - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getPoints() - Method in class edu.stanford.math.plex4.streams.utility.SkeletalMetric
getPrependIndex(Map<Integer, X>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
getProbabilities() - Method in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
getProbabilities(int, double) - Method in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph: We need one probability for each potential common ancestor depth d=1..k-1.
getProbabilities(int, double) - Method in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph: We need one probability for each potential common ancestor depth d=1..k-1.
getProbabilityPartition(int[]) - Method in class edu.stanford.math.plex4.graph.random.BAGraph: Constructs a partition p of [0,1] such that p[i+1]-p[i] is proportional to the degree of node i in the list d.
getProbabilityPartition(int[]) - Method in class edu.stanford.math.plex4.graph.random.PrescribedDegrees: Constructs a partition p of [0,1] such that p[i+1]-p[i] is proportional to the degree of node i in the list d.
getRandomCirclePoints(int) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function returns a point set containing n randomly selected points, ordered clockwise on a circle.
getRandomFigure8Points(int) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function returns randomly generated points on a figure-8 in the plane.
getRandomIntInRange(int, int) - Method in class edu.stanford.math.plex4.graph.random.ClusteredERGraph
getRandomSpherePoints(int, int) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function returns n uniformly random point on the d-dimensional sphere as a subset of R^{d+1}.
getRandomSphereProductPoints(int, int, int) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function returns uniformly distributed points on the space S^k x ...
getRandomTorusPoints(int, double, double) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function returns non-uniformly generated points on the torus in R^3.
getRandomTrefoilKnotPoints(int) - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples
getRangeMax() - Method in class edu.stanford.math.plex4.streams.filter.RandomProjectionFilterFunction
getRationalCellularAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getRationalCellularAlgorithm(int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function returns a cellular persistence algorithm over the the rational numbers.
getRationalCellularClassicalHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getRationalCellularRelativeHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getRationalHomAlgorithm() - Static method in class edu.stanford.math.plex4.api.Plex4: This function creates a persistent homology algorithm over the rationals for computing homology of simplicial hom complexes.
getRationalSimplexPairAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getRationalSimplexPairClassicalHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getRationalSimplexPairRelativeHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getRationalSimplicialAbsoluteHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getRationalSimplicialAlgorithm(int) - Static method in class edu.stanford.math.plex4.api.Plex4: This function returns a simplicial persistence algorithm over the the rational numbers.
getRationalSimplicialClassicalHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getRationalSimplicialRelativeHomology(int) - Static method in class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
getRelativeCohomologyBarcodes() - Method in class edu.stanford.math.plex4.examples.DeSilvaMorozovJohanssonExample: This function returns the correct relative cohomology barcodes along with the generators.
getRelativeHomologyBarcodes() - Method in class edu.stanford.math.plex4.examples.DeSilvaMorozovJohanssonExample: This function returns the correct relative homology barcodes along with the generators.
getReverseEdge() - Method in class edu.stanford.math.plex4.bottleneck.FlowEdge
getRight() - Method in class edu.stanford.math.plex4.kd.KDNode
getRootedGraphSize() - Method in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph
getRow(Map<X, IntSparseFormalSum<Y>>, Y) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
getSecondGradedProjectionMap(IntAlgebraicFreeModule, IntAlgebraicFreeModule<V>) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.InducedHomologyMappingUtility
getSignOfLast() - Method in class edu.stanford.math.plex.SimplexFaceIterator: Return the sign of the last face -- only useful when codimension is 1.
getSimplex(int[]) - Static method in class edu.stanford.math.plex.Simplex: Get the simplex for a given set of vertices.
getSimplex(int[], int) - Static method in class edu.stanford.math.plex.Simplex: Get the simplex for a given set of vertices, including setting findex.
getSimplexPresorted(int[]) - Static method in class edu.stanford.math.plex.Simplex: Get the simplex for an already verified array of vertices.
getSimplexPresorted(int[], int) - Static method in class edu.stanford.math.plex.Simplex: Get the simplex for an already verified array of vertices, including setting findex.
getSimplicialSphere(int) - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function returns a static simplicial complex containing an n-sphere.
getSize() - Method in class edu.stanford.math.plex4.interop.Plex3Stream
getSize() - Method in class edu.stanford.math.plex4.streams.derived.DualStream
getSize() - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
getSize() - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
getSize() - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
getSize() - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function returns the total number of elements in the stream.
getSize() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
getSize() - Method in interface edu.stanford.math.plex4.streams.multi.AbstractMultifilteredStream: This function returns the total number of elements in the stream.
getSize() - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
getSize() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
getSize() - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
getSize() - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function returns the number of elements in the storage structure.
getSkeleton(AbstractFilteredStream<T>, int) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function dumps the k-skeleton of a chain complex into a list.
getSkeletonSize(AbstractFilteredStream<T>, int) - Static method in class edu.stanford.math.plex4.streams.utility.StreamUtility: This function computes the size of the k-skeleton of a chain complex.
getSortedStorageStructure(Comparator<T>) - Static method in class edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructureFactory: This function creates a new sorted storage structure.
getSource() - Method in class edu.stanford.math.plex4.bottleneck.FlowEdge
getSparseAdjacencyMatrix(AbstractUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility: This function computes the adjacency matrix of the given graph.
getSparseAdjacencyMatrix(AbstractWeightedUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility: This function computes the adjacency matrix of the given graph.
getSparseLaplacianMatrix(AbstractUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility: This function computes the Laplacian matrix of a graph.
getSparseLaplacianMatrix(AbstractWeightedUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility: This function computes the Laplacian matrix of a graph.
getSplitAxis() - Method in class edu.stanford.math.plex4.kd.KDNode
getSquare() - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function produces a square in the plane.
getStart() - Method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns the start of the interval.
getStart() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
getState() - Method in interface edu.stanford.math.plex4.homology.zigzag.AbstractHomologyTracker
getState() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
getState() - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
getStateWithoutFiniteBarcodes() - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
getStateWithoutFiniteBarcodes(int) - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
getSubset(int) - Method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.VietorisRipsBootstrapper
getSubset(double[][], int[]) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
getTetrahedron() - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function returns a simplicial tetrahedron (which happens to be equal to a simplicial 2-sphere).
getTetrahedronVertices() - Static method in class edu.stanford.math.plex4.examples.PointCloudExamples: This function returns the vertices of an tetrahedron.
getTitle() - Method in class edu.stanford.math.plex4.io.Table: This function returns the title of the table.
getTorus() - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function returns a simplicial 2-torus.
getTreeDepth(int) - Method in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph: We want to construct the smallest binary tree of size 2^{d+1}-1 (d>0) such that there are at least n leaves.
getTriangle() - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function returns a simplicial triangle (which happens to be equal to a simplicial 1-sphere).
getUnderlyingMetricSpace() - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
getUniqueCategoryOutputPath(String) - Static method in class edu.stanford.math.plex4.io.FileManager: This function returns a unique category output path for the specified category.
getUniqueFilePath(String, String) - Static method in class edu.stanford.math.plex4.io.FileManager
getUniqueOutputPath() - Static method in class edu.stanford.math.plex4.io.FileManager: This function returns a unique output path.
getUnweightedAdjacencySets() - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
getValues() - Method in class edu.stanford.math.plex4.streams.filter.EccentricityFilterFunction
getValues() - Method in class edu.stanford.math.plex4.streams.filter.ExplicitIntFilterFunction
getValues() - Method in interface edu.stanford.math.plex4.streams.filter.IntFilterFunction
getValues() - Method in class edu.stanford.math.plex4.streams.filter.KernelDensityFilterFunction
getValues() - Method in class edu.stanford.math.plex4.streams.filter.RandomProjectionFilterFunction
getVertices() - Method in class edu.stanford.math.plex4.homology.chain_basis.Simplex: This function returns an array containing the vertices of the simplex.
getWeight(int, int) - Method in interface edu.stanford.math.plex4.graph.AbstractWeightedUndirectedGraph: This function returns the weight of the edge (i, j).
getWeight(int, int) - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
getWitnessAndDistance(int...) - Method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
getZomorodianCarlssonExample() - Static method in class edu.stanford.math.plex4.examples.SimplexStreamExamples: This function returns a filtered simplicial complex which is shown in Figure 1 of the paper "Computing Persistent Homology" by Zomorodian and Carlsson.
granularity - Variable in class edu.stanford.math.plex.LazyWitnessStream
granularity - Variable in class edu.stanford.math.plex.RipsStream: The granularity used in assigning filtration indices to simplices.
granularity - Variable in class edu.stanford.math.plex.WitnessStream
GraphDotWriter - Class in edu.stanford.math.plex4.graph.io
GraphDotWriter() - Constructor for class edu.stanford.math.plex4.graph.io.GraphDotWriter
graphImplementation - Variable in class edu.stanford.math.plex4.graph.random.GraphInstanceGenerator
GraphInstanceGenerator - Class in edu.stanford.math.plex4.graph.random: This class abstracts the construction of graphs.
GraphInstanceGenerator() - Constructor for class edu.stanford.math.plex4.graph.random.GraphInstanceGenerator
GraphInstanceGenerator(GraphInstanceGenerator.ImplementationType) - Constructor for class edu.stanford.math.plex4.graph.random.GraphInstanceGenerator
GraphInstanceGenerator.ImplementationType - Enum in edu.stanford.math.plex4.graph.random
GraphMetricFactory - Interface in edu.stanford.math.plex4.graph.metric: This interface defines the functionality of a factory which creates a metric space on a given graph.
GraphUtility - Class in edu.stanford.math.plex4.graph.utility: This class contains various static functions for manipulating graphs.
GraphUtility() - Constructor for class edu.stanford.math.plex4.graph.utility.GraphUtility
greatCircleDistance(double, double, double, double) - Static method in class edu.stanford.math.plex4.utility.MathUtility: This function returns the great circle distance (geodesic distance) between two points on the unit sphere.
greatCircleDistance(double[], double[]) - Static method in class edu.stanford.math.plex4.utility.MathUtility: This function returns the great circle distance between two points on the unit sphere given their rectangular coordinates.
gridHeight - Variable in class edu.stanford.math.plex.BCPlot
gridIsVisible - Variable in class edu.stanford.math.plex.BCPlot
gridOff() - Method in class edu.stanford.math.plex4.io.MatlabWriter
gridOn() - Method in class edu.stanford.math.plex4.io.MatlabWriter
gridRulerFont - Variable in class edu.stanford.math.plex.BCPlot
gridRulerFontColor - Variable in class edu.stanford.math.plex.BCPlot
gridRulerFontMetrics - Variable in class edu.stanford.math.plex.BCPlot
gridTickMajorColor - Variable in class edu.stanford.math.plex.BCPlot
gridTickMinorColor - Variable in class edu.stanford.math.plex.BCPlot
gridWidth - Variable in class edu.stanford.math.plex.BCPlot
grow(int) - Method in class edu.stanford.math.plex4.homology.nonautogen.DisjointSetSystem: Deprecated.
grow_table(int) - Method in class edu.stanford.math.plex.SimplexTable

H

HalfplaneFlattener<T extends PrimitiveBasisElement> - Class in edu.stanford.math.plex4.streams.multi: This flattener maps a filtration value vector, x, to the smallest integer k such that <= k where p is the specified principal direction.
HalfplaneFlattener(double[]) - Constructor for class edu.stanford.math.plex4.streams.multi.HalfplaneFlattener
has_next_index() - Method in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
hash32(byte[]) - Static method in class edu.stanford.math.plex.CRC: Compute 32-bit CRC for an array of bytes.
hash32(short[]) - Static method in class edu.stanford.math.plex.CRC: Compute 32-bit CRC for an array of shorts.
hash32(int[]) - Static method in class edu.stanford.math.plex.CRC: Compute 32-bit CRC for an array of ints.
hash32(float[]) - Static method in class edu.stanford.math.plex.CRC: Compute 32-bit CRC for an array of float.
hash32(long[]) - Static method in class edu.stanford.math.plex.CRC: Compute 32-bit CRC for an array of longs.
hash32(double[]) - Static method in class edu.stanford.math.plex.CRC: Compute 32-bit CRC for an array of double.
hash32(double[][], int, int) - Static method in class edu.stanford.math.plex.CRC: Compute 32-bit CRC for a matrix of doubles.
hash32(long, int) - Static method in class edu.stanford.math.plex.CRC: Easily testable function which computes 32-bit CRC for a single long.
hash32tab0 - Static variable in class edu.stanford.math.plex.CRC: Internal table used by CRC code.
hash64(byte[]) - Static method in class edu.stanford.math.plex.CRC: Compute 64-bit CRC for an array of bytes.
hash64(short[]) - Static method in class edu.stanford.math.plex.CRC: Compute 64-bit CRC for an array of shorts.
hash64(int[]) - Static method in class edu.stanford.math.plex.CRC: Compute 64-bit CRC for an array of ints.
hash64(float[]) - Static method in class edu.stanford.math.plex.CRC: Compute 64-bit CRC for an array of float.
hash64(long[]) - Static method in class edu.stanford.math.plex.CRC: Compute 64-bit CRC for an array of longs.
hash64(double[]) - Static method in class edu.stanford.math.plex.CRC: Compute 64-bit CRC for an array of double.
hash64(long, long) - Static method in class edu.stanford.math.plex.CRC: Easily testable function which computes 64-bit CRC for a single long.
hash64tab0 - Static variable in class edu.stanford.math.plex.CRC: Internal table used by CRC code.
hash64tab1 - Static variable in class edu.stanford.math.plex.CRC: Internal table used by CRC code.
HashCode() - Method in class edu.stanford.math.plex.Chain: Because we override equals, we also need to override HashCode.
hashCode() - Method in class edu.stanford.math.plex.Packed2Simplex: Overrides Object hashcode.
hashCode() - Method in class edu.stanford.math.plex.Packed4Simplex: Overrides Object hashcode.
hashCode() - Method in class edu.stanford.math.plex.Packed6Simplex: Overrides Object hashcode.
hashCode() - Method in class edu.stanford.math.plex.Packed8Simplex: Overrides Object hashcode.
hashCode() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Float: Overrides Object hashcode.
hashCode() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Int: Overrides Object hashcode.
hashCode() - Method in class edu.stanford.math.plex.PersistenceInterval.Float: Overrides Object hashcode.
hashCode() - Method in class edu.stanford.math.plex.PersistenceInterval.Int: Overrides Object hashcode.
hashCode() - Method in class edu.stanford.math.plex.Simplex: Overrides Object hashcode.
hashCode() - Method in class edu.stanford.math.plex4.bottleneck.FlowEdge
hashCode() - Method in class edu.stanford.math.plex4.homology.barcodes.Interval
hashCode() - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor
hashCode() - Method in class edu.stanford.math.plex4.homology.chain_basis.Cell
hashCode() - Method in class edu.stanford.math.plex4.homology.chain_basis.Simplex
hashCode() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
hashCode() - Method in class edu.stanford.math.plex4.visualization.Point2D
HashedStorageStructure<T extends PrimitiveBasisElement> - Class in edu.stanford.math.plex4.streams.storage_structures: This class provides a stream storage mechanism that is based on a multi-layer map.
HashedStorageStructure(Comparator<T>) - Constructor for class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure: This construction initializes the class with a comparator for comparing the basis elements.
HashedStorageStructureIterator<E> - Class in edu.stanford.math.plex4.streams.storage_structures: This class implements the Iterator interface for a HashedStorageStructure.
HashedStorageStructureIterator(TIntObjectHashMap<TIntObjectHashMap<List<E>>>) - Constructor for class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructureIterator: This constructor accepts a filtration index -> dimension -> list mapping.
hasNext() - Method in class edu.stanford.math.plex.Cone
hasNext() - Method in class edu.stanford.math.plex.ExplicitStream.DComplex: Is there a larger dimensional DComplex for this stream?
hasNext() - Method in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator: Returns true if the iterator has more simplices.
hasNext() - Method in class edu.stanford.math.plex.ExplicitStream: Is there a next Simplex in the stream?
hasNext() - Method in class edu.stanford.math.plex.LazyWitnessStream: Is there a next Simplex in the stream?
hasNext() - Method in class edu.stanford.math.plex.PointData.Discrete.DSS
hasNext() - Method in class edu.stanford.math.plex.RipsStream: Is there a next Simplex in the stream?
hasNext() - Method in class edu.stanford.math.plex.SimplexFaceIterator
hasNext() - Method in class edu.stanford.math.plex.SimplexStream: Is there a next Simplex in the stream?
hasNext() - Method in class edu.stanford.math.plex.SimplexStream.Stack: Is there a next Simplex in the stream?
hasNext() - Method in class edu.stanford.math.plex.SimplexStream.Stack.StackIterator: Returns true if the iterator has more simplices.
hasNext() - Method in class edu.stanford.math.plex.SimplexTable.SimpleTableIterator: Returns true if the iterator has more simplices.
hasNext() - Method in class edu.stanford.math.plex.TmpStream: Returns true if the stream has more simplices.
hasNext() - Method in class edu.stanford.math.plex.WitnessStream: Is there a next Simplex in the stream?
hasNext() - Method in class edu.stanford.math.plex4.graph.UndirectedListEdgeIterator
hasNext() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructureIterator
hasNext() - Method in class edu.stanford.math.plex4.streams.storage_structures.IntOrderedIterator
hasPerfectMatching() - Method in class edu.stanford.math.plex4.bottleneck.WeightedBipartiteGraph
heightOfBaseRegionUsedForPlotLegendRulerLabels - Variable in class edu.stanford.math.plex.BCPlot
hgLeafCount - Variable in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph
HierarchicalClustering - Class in edu.stanford.math.clustering
HierarchicalClustering(AbstractIntMetricSpace) - Constructor for class edu.stanford.math.clustering.HierarchicalClustering
HierarchicalERGraph - Class in edu.stanford.math.plex4.graph.random
HierarchicalERGraph(int, int, double, double) - Constructor for class edu.stanford.math.plex4.graph.random.HierarchicalERGraph: Note: n and m should each be a power of 2
HIGH_PRECISION - Static variable in class edu.stanford.math.plex4.utility.ComparisonUtility
highlightGenerator(BooleanSparseFormalSum<Simplex>, Color) - Method in class edu.stanford.math.plex4.visualization.HomologyGeneratorVisualizer
HistogramCreator - Class in edu.stanford.math.mapper
holdOff() - Method in class edu.stanford.math.plex4.io.MatlabWriter
holdOn() - Method in class edu.stanford.math.plex4.io.MatlabWriter
HomologyBasisTracker - Class in edu.stanford.math.plex4.homology.zigzag: This class maintains the right-filtration for performing zig-zag homology.
HomologyBasisTracker(IntAbstractField, Comparator) - Constructor for class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker: This constructor initializes the object with a field and a comparator on the basis type.
HomologyGeneratorVisualizer - Class in edu.stanford.math.plex4.visualization
HomologyGeneratorVisualizer() - Constructor for class edu.stanford.math.plex4.visualization.HomologyGeneratorVisualizer
HomologyUtility - Class in edu.stanford.math.plex4.homology.utility: This class contains static utility functions to aid the homology computations.
HomologyUtility() - Constructor for class edu.stanford.math.plex4.homology.utility.HomologyUtility
HomologyVisualizer - Class in edu.stanford.math.plex4.visualization
HomologyVisualizer() - Constructor for class edu.stanford.math.plex4.visualization.HomologyVisualizer
HomStream<T,U> - Class in edu.stanford.math.plex4.streams.derived: This implements the hom-complex from two filtered chain complexes.
HomStream(AbstractFilteredStream<T>, AbstractFilteredStream) - Constructor for class edu.stanford.math.plex4.streams.derived.HomStream: This constructor initializes the hom-complexes from two existing chain complexes.
huberPenaltyFunction(double, double) - Static method in class edu.stanford.math.plex4.utility.MathUtility: This function computes the Huber penalty function of an input.

I

identifyPoints(ExplicitCellStream, int[]) - Static method in class edu.stanford.math.plex4.examples.CellComplexOperations: This function collapses the points in the supplied array to a single point.
IdentityConverter - Class in edu.stanford.math.plex4.homology.filtration: This class defines a filtration value conversion which simply defines the filtration value to be equal to the filtration index.
illegal_interval_string(int, double, double) - Static method in class edu.stanford.math.plex.BCPlot
ImageRegion - Class in edu.stanford.math.plex4.visualization
ImageRegion() - Constructor for class edu.stanford.math.plex4.visualization.ImageRegion
ImageRegion.Double - Class in edu.stanford.math.plex4.visualization
ImageRegion.Double(double, double, double, double) - Constructor for class edu.stanford.math.plex4.visualization.ImageRegion.Double
ImageRegion.Int - Class in edu.stanford.math.plex4.visualization
ImageRegion.Int(int, int, int, int) - Constructor for class edu.stanford.math.plex4.visualization.ImageRegion.Int
implementationType - Variable in class edu.stanford.math.plex4.graph.random.GraphInstanceGenerator
importFromFile(String) - Method in class edu.stanford.math.plex4.io.DoubleArrayReaderWriter
importFromFile(String) - Method in interface edu.stanford.math.plex4.io.ObjectReader
importFromFile(String) - Method in class edu.stanford.math.plex4.io.ObjReader
importFromFile(String) - Method in class edu.stanford.math.plex4.io.SimplexStreamReaderWriter
include(AbstractHomologyTracker<Integer, I, ?, IntSparseFormalSum>, AbstractHomologyTracker<Integer, I, ?, IntSparseFormalSum>, AbstractHomologyTracker<Integer, I, ?, IntSparseFormalSum>, IntervalTracker<Integer, I, IntSparseFormalSum>, IntAlgebraicFreeModule, I, I) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.InducedHomologyMappingUtility
IncreasingLinearConverter - Class in edu.stanford.math.plex4.homology.filtration: This class implements a conversion between filtration values and filtration indices that is linear and increasing.
IncreasingLinearConverter(int, double, double) - Constructor for class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter: This constructor initializes the object with the number of divisions in the range, and the minimum and maximum values.
IncreasingLinearConverter(int, double) - Constructor for class edu.stanford.math.plex4.homology.filtration.IncreasingLinearConverter: This initializes the object with a default minimum filtration value of zero.
IncreasingOrthantFlattener<T extends PrimitiveBasisElement> - Class in edu.stanford.math.plex4.streams.multi
IncreasingOrthantFlattener(double[]) - Constructor for class edu.stanford.math.plex4.streams.multi.IncreasingOrthantFlattener
incrementalExpansion(UndirectedWeightedListGraph, int) - Method in class edu.stanford.math.plex4.streams.impl.FlagComplexStream: This function performs the incremental expansion of the complex.
incrementFlow(FlowEdge, int) - Method in class edu.stanford.math.plex4.bottleneck.FlowNetwork
indexedComparator - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
indexedComparator - Variable in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker: This comparator provides the dictionary ordering on filtration value - basis element pairs.
indexMapping - Variable in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector: This array holds the mapping between the indices of the landmark points, and the indices within the metric space.
indexSelections - Variable in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
indices - Variable in class edu.stanford.math.plex4.streams.impl.FlagComplexStream
indices - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream
InducedHomologyMappingUtility - Class in edu.stanford.math.plex4.homology.zigzag.bootstrap
InducedHomologyMappingUtility() - Constructor for class edu.stanford.math.plex4.homology.zigzag.bootstrap.InducedHomologyMappingUtility
infiniteExtent() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Float: Is this PersistenceBasisInterval semi-infinite in extent?
infiniteExtent() - Method in class edu.stanford.math.plex.PersistenceBasisInterval: Is this PersistenceBasisInterval semi-infinite in extent?
infiniteExtent() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Int: Is this PersistenceBasisInterval semi-infinite in extent?
infiniteExtent() - Method in class edu.stanford.math.plex.PersistenceInterval.Float: Is this PersistenceInterval semi-infinite in extent?
infiniteExtent() - Method in class edu.stanford.math.plex.PersistenceInterval: Is this PersistenceInterval semi-infinite in extent?
infiniteExtent() - Method in class edu.stanford.math.plex.PersistenceInterval.Int: Is this PersistenceInterval semi-infinite in extent?
INFINITY - Static variable in class edu.stanford.math.clustering.HierarchicalClustering
init_okay(int[]) - Static method in class edu.stanford.math.plex.Plex.BettiNumbers
initializeFilteredComparator(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This function simply updates the filtered comparator to the one induced by the given filtered stream.
initializeFilteredComparator(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This function simply updates the filtered comparator to the one induced by the given filtered stream.
initializeFilteredComparator(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This function simply updates the filtered comparator to the one induced by the given filtered stream.
initializeFilteredComparator(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This function simply updates the filtered comparator to the one induced by the given filtered stream.
initializeFilteredComparator(AbstractFilteredStream) - Method in class edu.stanford.math.plex4.homology.zigzag.ZigZagHomology: This function simply updates the filtered comparator to the one induced by the given filtered stream.
initializeGraph(int) - Method in class edu.stanford.math.plex4.graph.random.GraphInstanceGenerator
initializeWithSeed(int) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function initializes the seeds of the random number generators to the specified values.
initJFrame() - Method in class edu.stanford.math.plex.BCPlot
insert(T, double) - Method in class edu.stanford.math.plex4.metric.impl.TruncatedPriorityQueue: This function inserts the given object (or index), with a specified value into the queue.
insertComments(String) - Method in class edu.stanford.math.plex4.io.MatlabWriter: This function modifies the input string so that it will be properly printed as a comment in Matlab.
IntAbsoluteHomology - Class in edu.stanford.math.plex4.autogen.homology
IntAbsoluteHomology(IntAbstractField, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.IntAbsoluteHomology: This constructor initializes the object with a field and a comparator on the basis type.
IntClassicalHomology - Class in edu.stanford.math.plex4.autogen.homology: This class performs the persistent homology algorithm as outlined in the paper "Computing Persistent Homology" by Zomorodian and Carlsson.
IntClassicalHomology(IntAbstractField, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.IntClassicalHomology: This constructor initializes the object with a field and a comparator on the basis type.
integerChainModule - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
integerComparator - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
internalExternalIndexMap - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
internalIndex - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
intersect(TIntHashSet, TIntHashSet) - Static method in class edu.stanford.math.plex4.utility.ComparisonUtility: This function computes the intersection of two sets.
intersection_count(int[], int[]) - Static method in class edu.stanford.math.plex.Plex
intersectionGraph(List<TIntHashSet>) - Static method in class edu.stanford.math.mapper.MapperPipeline
Interval<T extends java.lang.Comparable<T>> - Class in edu.stanford.math.plex4.homology.barcodes: This class implements the functionality of an interval of values of any comparable type.
IntervalDescriptor<T,G> - Class in edu.stanford.math.plex4.homology.zigzag
IntervalDescriptor(T, int, G) - Constructor for class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
intervalGeneratorPairs - Variable in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor
IntervalLengthComparator - Class in edu.stanford.math.plex4.homology.barcodes
intervals - Variable in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor
intervalTracker - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
IntervalTracker<K,I extends java.lang.Comparable,G> - Class in edu.stanford.math.plex4.homology.zigzag
IntervalTracker() - Constructor for class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
intField - Variable in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
IntFilterFunction - Interface in edu.stanford.math.plex4.streams.filter
IntOrderedIterator<E> - Class in edu.stanford.math.plex4.streams.storage_structures: This class provides iteration over the second component of each element in an Iterable collection of type IntObjectPair.
IntOrderedIterator(Iterable<IntObjectPair<E>>) - Constructor for class edu.stanford.math.plex4.streams.storage_structures.IntOrderedIterator: This constructor initializes the iterator with an iterable collection over the type IntObjectPair.
IntPersistenceAlgorithm - Class in edu.stanford.math.plex4.autogen.homology: This class defines the functionality for a persistence algorithm with underlying field type being int and underlying basis element type being U.
IntPersistenceAlgorithm(IntAbstractField, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This constructor initializes the object with a field and a comparator on the basis type.
IntPersistentHomology - Class in edu.stanford.math.plex4.autogen.homology: This class defines the functionality for a persistence algorithm with underlying field type being int and underlying basis element type being U.
IntPersistentHomology(IntAbstractField, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.IntPersistentHomology: This constructor initializes the object with a field and a comparator on the basis type.
IntRelativeHomology - Class in edu.stanford.math.plex4.autogen.homology
IntRelativeHomology(IntAbstractField, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.IntRelativeHomology: This constructor initializes the object with a field and a comparator on the basis type.
invoke(Interpreter, CallStack) - Static method in class bsh.commands.log: Implement log() command.
invoke(Interpreter, CallStack, String) - Static method in class bsh.commands.log: Implement log(String logfile_name) command.
invoke(Interpreter, CallStack, boolean) - Static method in class bsh.commands.log: Implement log(boolean on_flag) command.
invoke(Interpreter, CallStack, String) - Static method in class bsh.commands.setLogging: Implement setLogging(String default_dir) command.
invoke(Interpreter, CallStack, boolean) - Static method in class bsh.commands.setLogging: Implement setLogging(boolean default_on_flag) command.
is_permutation(int[]) - Static method in class edu.stanford.math.plex.Plex
isBoundary(G) - Method in interface edu.stanford.math.plex4.homology.zigzag.AbstractHomologyTracker
isBoundary(IntSparseFormalSum) - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
isBoundary(IntSparseFormalSum) - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
isCycle(IntSparseFormalSum) - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
isFinalized() - Method in class edu.stanford.math.plex4.interop.Plex3Stream
isFinalized() - Method in class edu.stanford.math.plex4.streams.derived.DualStream
isFinalized() - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
isFinalized() - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
isFinalized() - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
isFinalized() - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function checks whether the finalize() function has been called.
isFinalized() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
isFinalized() - Method in interface edu.stanford.math.plex4.streams.multi.AbstractMultifilteredStream: This function checks whether the finalize() function has been called.
isFinalized() - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
isFinalized() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
isFinalized() - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
isFinalized() - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function returns true if the stream has been finalized.
isGraphical(int[]) - Static method in class edu.stanford.math.plex4.graph.random.PrescribedDegrees: Determines if a degree sequence is realizable using the Erdos-Gallai Criteria
isInfinite() - Method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function indicates whether the interval is infinite (either left or right infinite, or both).
isLeftClosed() - Method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function indicates whether the interval is closed on the left.
isLeftInfinite() - Method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function indicates whether the interval is left-infinite.
isMonotoneIncreasing(int[]) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
isRightClosed() - Method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function indicates whether the interval is closed on the right.
isRightInfinite() - Method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function indicates whether the interval is right-infinite.
isWitness(int, Simplex) - Method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
isWitness(int, int[]) - Method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
isZero(Chain) - Static method in class edu.stanford.math.plex.Chain
isZero() - Method in class edu.stanford.math.plex.Chain
iterator() - Method in class edu.stanford.math.mapper.BoundedIntervalCover
iterator() - Method in class edu.stanford.math.mapper.FiniteMetricSpaceCover
iterator() - Method in class edu.stanford.math.mapper.SetCover1D
iterator() - Method in class edu.stanford.math.plex.Cone
iterator() - Method in class edu.stanford.math.plex.ExplicitStream: Make an iterator for the stream.
iterator(int) - Method in class edu.stanford.math.plex.ExplicitStream: Make an iterator for the stream elements of fixed dimension.
iterator() - Method in class edu.stanford.math.plex.LazyWitnessStream: Make an iterator for the stream.
iterator() - Method in class edu.stanford.math.plex.PointData.Discrete.DSS: Make an iterator for the stream.
iterator() - Method in class edu.stanford.math.plex.RipsStream: Make an iterator for the stream.
iterator(int) - Method in class edu.stanford.math.plex.RipsStream: Make an iterator for the stream elements of fixed dimension.
iterator() - Method in class edu.stanford.math.plex.SimplexStream.Stack: Make a non-destructive iterator for the Stack.
iterator(int) - Method in class edu.stanford.math.plex.SimplexStream.Stack: Make a non-destructive iterator for fixed dimensional entries in the Stack.
iterator() - Method in class edu.stanford.math.plex.SimplexTable: Make an iterator for the table.
iterator() - Method in class edu.stanford.math.plex.TmpStream
iterator() - Method in class edu.stanford.math.plex.WitnessStream: Make an iterator for the stream.
iterator() - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph: This function returns an edge iterator that allows the user to iterate over the set of edges in the graph.
iterator() - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph
iterator() - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
iterator() - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor
iterator() - Method in class edu.stanford.math.plex4.interop.Plex3Stream
iterator() - Method in class edu.stanford.math.plex4.streams.derived.DualStream
iterator() - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
iterator() - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
iterator() - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
iterator() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream
iterator() - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
iterator() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
iterator() - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure

J

join(AbstractPersistenceTracker<K, I, G1>, AbstractPersistenceTracker<K, I, G2>, Map<K, K>, I, boolean) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.InducedHomologyMappingUtility
JPlex - Class in bsh: The JPlex class is the entry point for Plex users into Beanshell.
JPlex() - Constructor for class bsh.JPlex
JTerm - Class in bsh: The JTerm class is the entry point for Plex users into Beanshell who want a simple "terminal" interface (no windows, menus, etc.).
JTerm() - Constructor for class bsh.JTerm

K

k - Variable in class edu.stanford.math.plex.SimplexFaceIterator
k - Variable in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
KDEuclideanMetricSpace - Class in edu.stanford.math.plex4.kd: This class implements the AbstractSearchableMetricSpace interface for providing query functions for a Euclidean metric space.
KDEuclideanMetricSpace(double[][]) - Constructor for class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
KDNode - Class in edu.stanford.math.plex4.kd: This class contains the functionality of a node within a KD-tree.
KDNode(int, int) - Constructor for class edu.stanford.math.plex4.kd.KDNode
KDTree - Class in edu.stanford.math.plex4.kd: This class implements the functionality of a KD-tree.
KDTree(double[][]) - Constructor for class edu.stanford.math.plex4.kd.KDTree: Constructor for initializing the KD-tree with a set of points.
KernelDensityFilterFunction - Class in edu.stanford.math.plex4.streams.filter
KernelDensityFilterFunction(AbstractIntMetricSpace, double) - Constructor for class edu.stanford.math.plex4.streams.filter.KernelDensityFilterFunction
keyPressed() - Method in class edu.stanford.math.plex4.visualization.AbstractVisualizer: On keypress: Implement state changes and other effects as needed.
KNearestNeighborsGraph - Class in edu.stanford.math.plex4.graph.random: Generates n random points in [0,1]^d and connects each point to its k-nearest neighbors
KNearestNeighborsGraph(int, int, int) - Constructor for class edu.stanford.math.plex4.graph.random.KNearestNeighborsGraph

L

l - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonNode
L - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
L - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream
L1 - Variable in class edu.stanford.math.plex4.streams.impl.WitnessBicomplex
L2 - Variable in class edu.stanford.math.plex4.streams.impl.WitnessBicomplex
labelFont - Variable in class edu.stanford.math.plex.BCPlot
labelFontColor - Variable in class edu.stanford.math.plex.BCPlot
labelFontMetrics - Variable in class edu.stanford.math.plex.BCPlot
landmarks - Variable in class edu.stanford.math.plex.LazyWitnessStream
landmarks - Variable in class edu.stanford.math.plex.WitnessStream
LandmarkSelector<T> - Class in edu.stanford.math.plex4.metric.landmark: This abstract class defines the functionality of a landmark set within an arbitrary finite metric space.
LandmarkSelector(AbstractSearchableMetricSpace<T>, int) - Constructor for class edu.stanford.math.plex4.metric.landmark.LandmarkSelector: This constructor initializes the landmark selector with a finite metric space, and a size parameter.
LandmarkSelector(AbstractSearchableMetricSpace<T>, int[]) - Constructor for class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
landmarkSelector - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream: This is the selection of landmark points
landmarkSelector - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream: This is the selection of landmark points
landmarkSetSize - Variable in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector: This is the size of the landmark set
LazyWitnessStream - Class in edu.stanford.math.plex: A LazyWitnessStream is a SimplexStream whose elements are the simplices of the lazy Witness complex of a PointData instance.
LazyWitnessStream() - Constructor for class edu.stanford.math.plex.LazyWitnessStream
LazyWitnessStream(double, int, double, int, int[], PointData) - Static method in class edu.stanford.math.plex.Plex: Make a stream of the simplices in a lazy Witness complex for data.
LazyWitnessStream<T> - Class in edu.stanford.math.plex4.streams.impl: This class implements the lazy witness complex described in the paper "Topological estimation using witness complexes", by Vin de Silva and Gunnar Carlsson.
LazyWitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double, int, int) - Constructor for class edu.stanford.math.plex4.streams.impl.LazyWitnessStream: Constructor which initializes the complex with a metric space.
LazyWitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double, int) - Constructor for class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
LazyWitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double, int, int[]) - Constructor for class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
LazyWitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double, int[]) - Constructor for class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
LazyWitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double[], int) - Constructor for class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
LazyWitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double[]) - Constructor for class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
LazyWitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double[], int, int[]) - Constructor for class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
LazyWitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double[], int[]) - Constructor for class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
leftMargin - Variable in class edu.stanford.math.plex.BCPlot
legendMajorFont - Variable in class edu.stanford.math.plex.BCPlot
legendMajorFontColor - Variable in class edu.stanford.math.plex.BCPlot
legendMajorFontMetrics - Variable in class edu.stanford.math.plex.BCPlot
legendMajorString - Variable in class edu.stanford.math.plex.BCPlot
legendMinorFont - Variable in class edu.stanford.math.plex.BCPlot
legendMinorFontColor - Variable in class edu.stanford.math.plex.BCPlot
legendMinorFontMetrics - Variable in class edu.stanford.math.plex.BCPlot
legendMinorString - Variable in class edu.stanford.math.plex.BCPlot
lengths_array - Variable in class edu.stanford.math.plex.RipsStream
lessThan(SimplexStream.Head) - Method in class edu.stanford.math.plex.SimplexStream.Head: Compare one Head to another.
limit() - Method in class edu.stanford.math.plex.SimplexTable: The number of simplices that can be interned before growing the table.
LinkageTree - Class in edu.stanford.math.clustering
LinkageTree() - Constructor for class edu.stanford.math.clustering.LinkageTree
linkClusters(int, int, int) - Method in class edu.stanford.math.plex4.graph.random.ClusteredERGraph: Warning: No input validation is performed.
linkClustersInPlace(AbstractUndirectedGraph, int, int, int, int, int) - Method in class edu.stanford.math.plex4.graph.random.ClusteredERGraph
LOAD_FACTOR - Static variable in class edu.stanford.math.plex.SimplexTable
loadObject(String) - Static method in class edu.stanford.math.plex4.io.FileIOUtility
log - Class in bsh.commands: Turn on/off input logging in the current interpreter, specify the specific log file to use, or return the logging status string.
log() - Constructor for class bsh.commands.log
log(String...) - Static method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
log_status() - Method in class bsh.PlexReader: Return a String describing the logging status, including defaults.
logStatus() - Method in class bsh.PlexInterpreter: Return the status string
low(BooleanSparseFormalSum) - Method in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This function computes the operation low_A(j) as described in the paper.
low(IntSparseFormalSum) - Method in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This function computes the operation low_A(j) as described in the paper.
low(ObjectSparseFormalSum<F, U>) - Method in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This function computes the operation low_A(j) as described in the paper.
low(IntSparseFormalSum<X>, Comparator<X>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function computes the operation low_A(j) as described in the paper.
LOW_PRECISION - Static variable in class edu.stanford.math.plex4.utility.ComparisonUtility
lowerEntries(int[], int) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility: This function returns the first k entries of the supplied array.

M

m - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
m - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream
m_index(int, int, int) - Static method in class edu.stanford.math.plex.WitnessStream
main(String[]) - Static method in class bsh.JPlex: The arguments to main are ignored.
main(String[]) - Static method in class bsh.JTerm: The arguments to main are ignored.
main(String[]) - Static method in class edu.stanford.math.plex.Plex: Entry point to Plex from the java interpreter.
main(String[]) - Static method in class edu.stanford.math.plex4.api.Plex4: Empty main function for convenience only.
main(String[]) - Static method in class edu.stanford.math.plex4.generation.GeneratorDriver
main(String[]) - Static method in class edu.stanford.math.plex4.visualization.HomologyGeneratorVisualizer
main(String[]) - Static method in class edu.stanford.math.plex4.visualization.HomologyVisualizer
make_empty_file(String, int) - Static method in class edu.stanford.math.plex.MappedBufferData
makeClusterInPlace(AbstractUndirectedGraph, int, int, double) - Method in class edu.stanford.math.plex4.graph.random.ClusteredERGraph
makeEdge(int, int) - Static method in class edu.stanford.math.plex.Packed2Simplex
makeEdge(int, int, int) - Static method in class edu.stanford.math.plex.Simplex: Get the edge for a pair of vertices.
makeExplicit(SimplexStream) - Static method in class edu.stanford.math.plex.ExplicitStream: Convert a SimplexStream into an explicit one.
makeExplicit(SimplexStream) - Static method in class edu.stanford.math.plex.Plex: Convert a SimplexStream into an explicit one.
makeFiniteClosedInterval(T, T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a finite closed interval.
makeFiniteLeftOpenInterval(T, T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a finite left-open interval.
makeFiniteOpenInterval(T, T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a finite open interval.
makeFiniteRightOpenInterval(T, T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a finite right-open interval.
makeInterval(T, T, boolean, boolean, boolean, boolean) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns an interval with the desired parameters.
makeLeftInfiniteClosedInterval(T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a left-infinite closed interval.
makeLeftInfiniteLeftOpenInterval(T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a left-infinite left-open interval.
makeLeftInfiniteOpenInterval(T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a left-infinite open interval.
makeLeftInfiniteRightOpenInterval(T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a left-infinite right-open interval.
makeMonotone(int[]) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
makeNewMatlabWriter(String) - Static method in class edu.stanford.math.plex4.io.MatlabInterface: This function creates and returns a new MatlabWriter.
makePoint(int) - Static method in class edu.stanford.math.plex.Packed2Simplex
makePoint(int, int) - Static method in class edu.stanford.math.plex.Simplex: Turn a vertex into a 0-simplex.
makeRandomLandmarks(PointData, int) - Static method in class edu.stanford.math.plex.WitnessStream: Randomly choose a subset of a given PointData for use as landmarks.
makeRightInfiniteClosedInterval(T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a right-infinite closed interval.
makeRightInfiniteLeftOpenInterval(T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a right-infinite left-open interval.
makeRightInfiniteOpenInterval(T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a right-infinite open interval.
makeRightInfiniteRightOpenInterval(T) - Static method in class edu.stanford.math.plex4.homology.barcodes.Interval: This function returns a right-infinite right-open interval.
makeSimplex(int[]) - Static method in class edu.stanford.math.plex.Packed2Simplex
makeSimplex(int[]) - Static method in class edu.stanford.math.plex.Packed4Simplex
makeSimplex(int[]) - Static method in class edu.stanford.math.plex.Packed6Simplex
makeSimplex(int[]) - Static method in class edu.stanford.math.plex.Packed8Simplex
makeSimplex(int...) - Static method in class edu.stanford.math.plex4.homology.chain_basis.Simplex
makeSimplexPresorted(int[]) - Static method in class edu.stanford.math.plex.Packed2Simplex
makeSimplexPresorted(int[]) - Static method in class edu.stanford.math.plex.Packed4Simplex
makeSimplexPresorted(int[]) - Static method in class edu.stanford.math.plex.Packed6Simplex
makeSimplexPresorted(int[]) - Static method in class edu.stanford.math.plex.Packed8Simplex
makeStarterGraph(int, AbstractUndirectedGraph) - Method in class edu.stanford.math.plex4.graph.random.BAGraph: Make a starter graph, in this case a line TODO: what kind of starter graph??
ManifoldGraph - Class in edu.stanford.math.plex4.graph.random: This class is used to create a k-nearest neighbors graph on a manifold.
ManifoldGraph(int, int, int) - Constructor for class edu.stanford.math.plex4.graph.random.ManifoldGraph: Constructor for the ManifoldGraph class.
map_file(String, boolean) - Static method in class edu.stanford.math.plex.MappedBufferData
MappedBufferData - Class in edu.stanford.math.plex: The MappedBufferData class is another very simple implementation of NSpace.
MappedBufferData() - Constructor for class edu.stanford.math.plex.MappedBufferData
MappedBufferData(String, int, int, int, int) - Constructor for class edu.stanford.math.plex.MappedBufferData
MappedBufferData(String, int, int, boolean) - Constructor for class edu.stanford.math.plex.MappedBufferData
MappedBufferData(String) - Constructor for class edu.stanford.math.plex.MappedBufferData
MappedBufferData(String, boolean) - Constructor for class edu.stanford.math.plex.MappedBufferData
MappedBufferData(String, int) - Constructor for class edu.stanford.math.plex.MappedBufferData
MappedBufferData(String, int, int, double, double) - Constructor for class edu.stanford.math.plex.MappedBufferData
MappedBufferData(String, int, int, int) - Constructor for class edu.stanford.math.plex.MappedBufferData
MapperPipeline - Class in edu.stanford.math.mapper
MapperPipeline() - Constructor for class edu.stanford.math.mapper.MapperPipeline
MapperSpecifier - Class in edu.stanford.math.mapper
MapperSpecifier() - Constructor for class edu.stanford.math.mapper.MapperSpecifier
mask - Variable in class edu.stanford.math.plex.SimplexTable
matchingSimplices(int, int, SimplexStream.ComparisonType) - Method in class edu.stanford.math.plex.RipsStream: Return simplices of specified dimension that compare "favorably" with a given findex.
matchingSimplices(int, double, SimplexStream.ComparisonType) - Method in class edu.stanford.math.plex.RipsStream: Return simplices of specified dimension that compare "favorably" with a given length.
MathUtility - Class in edu.stanford.math.plex4.utility: This class contains various static utility functions relating to math.
MathUtility() - Constructor for class edu.stanford.math.plex4.utility.MathUtility
MatlabInterface - Class in edu.stanford.math.plex4.io: This class has static methods for creating Matlab files to visualize data.
MatlabInterface() - Constructor for class edu.stanford.math.plex4.io.MatlabInterface
MatlabWriter - Class in edu.stanford.math.plex4.io: This class encapsulates writing to Matlab files.
MatlabWriter(String) - Constructor for class edu.stanford.math.plex4.io.MatlabWriter: This constructor initializes the class to be ready to write to the file with the filename provided.
MAX_2_INDEX - Static variable in class edu.stanford.math.plex.Packed2Simplex
MAX_4_INDEX - Static variable in class edu.stanford.math.plex.Packed4Simplex
MAX_6_INDEX - Static variable in class edu.stanford.math.plex.Packed6Simplex
MAX_8_INDEX - Static variable in class edu.stanford.math.plex.Packed8Simplex
max_dimension - Variable in class edu.stanford.math.plex.PointData.Discrete.DSS
MAX_DISPLAYABLE_BARS - Static variable in class edu.stanford.math.plex.BCPlot
MAX_END - Static variable in class edu.stanford.math.plex.PersistenceBasisInterval.Float
MAX_END - Static variable in class edu.stanford.math.plex.PersistenceBasisInterval.Int
MAX_END - Static variable in class edu.stanford.math.plex.PersistenceInterval.Float
MAX_END - Static variable in class edu.stanford.math.plex.PersistenceInterval.Int
MAX_ENTRY_LIMIT - Variable in class edu.stanford.math.plex.SimplexTable
MAX_GRID_HEIGHT_PER_PAGE - Static variable in class edu.stanford.math.plex.BCPlot
MAX_TABLE_SIZE - Variable in class edu.stanford.math.plex.SimplexTable
maxAllowableDimension - Variable in class edu.stanford.math.plex4.streams.impl.FlagComplexStream: The maximum allowable dimension of the complex.
maxAllowableDimension - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream: The maximum allowable dimension of the complex.
maxApproximation(double, double, double) - Static method in class edu.stanford.math.plex4.utility.MathUtility
maxC() - Method in class edu.stanford.math.plex.Chain: Return the coefficient of the largetst basis element.
maxDimension() - Method in class edu.stanford.math.plex.Cone
maxDimension() - Method in class edu.stanford.math.plex.ExplicitStream: Max dimension of simplices in the stream.
maxDimension - Variable in class edu.stanford.math.plex.LazyWitnessStream
maxDimension() - Method in class edu.stanford.math.plex.LazyWitnessStream: Max dimension of simplices in the stream.
maxDimension() - Method in class edu.stanford.math.plex.PointData.Discrete.DSS
maxDimension - Variable in class edu.stanford.math.plex.RipsStream: The maximum dimension of a Simplex that will be admitted to the complex.
maxDimension() - Method in class edu.stanford.math.plex.RipsStream: Max dimension of simplices in the stream.
maxDimension() - Method in class edu.stanford.math.plex.SimplexStream: Max dimension of simplices in the stream.
maxDimension() - Method in class edu.stanford.math.plex.SimplexStream.Stack: Max dimension of simplices in the stream.
maxDimension() - Method in class edu.stanford.math.plex.TmpStream
maxDimension - Variable in class edu.stanford.math.plex.WitnessStream
maxDimension() - Method in class edu.stanford.math.plex.WitnessStream: Max dimension of simplices in the stream.
maxDimension - Variable in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This stores the maximum dimension for which to compute (co)homology.
maxDimension - Variable in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This stores the maximum dimension for which to compute (co)homology.
maxDimension - Variable in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This stores the maximum dimension for which to compute (co)homology.
maxDimension - Variable in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This stores the maximum dimension for which to compute (co)homology.
maxDimension - Variable in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
maxDimension - Variable in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
maxDimension - Variable in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
maxDimension - Variable in class edu.stanford.math.plex4.homology.zigzag.ZigZagHomology: This stores the maximum dimension for which to compute (co)homology.
maxDimension - Variable in class edu.stanford.math.plex4.streams.impl.WitnessBicomplex
maxDistance - Variable in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
maxDistance - Variable in class edu.stanford.math.plex4.streams.impl.FlexibleVietorisRipsStream: The maximum distance allowed between two connected vertices.
maxDistance - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream: The maximum distance allowed between two connected vertices.
maxDistance - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream: The maximum distance allowed between two connected vertices.
maxFlow(int, int) - Method in class edu.stanford.math.plex4.bottleneck.FlowNetwork
maxFlow(FordFulkersonNode[], FordFulkersonEdge[], int, int) - Method in class edu.stanford.math.plex4.bottleneck.FordFulkerson: Inputs a graph to compute max flow/min cut for.
maxLen - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream
maxLog2(int) - Static method in class edu.stanford.math.plex4.utility.MathUtility
MaxMinLandmarkSelector<T> - Class in edu.stanford.math.plex4.metric.landmark: This class implements sequential max-min landmark selection of points from a metric space.
MaxMinLandmarkSelector(AbstractSearchableMetricSpace<T>, int) - Constructor for class edu.stanford.math.plex4.metric.landmark.MaxMinLandmarkSelector: This constructor initializes the landmark selector with a finite metric space, and a size parameter.
MaxMinLandmarkSelector(AbstractSearchableMetricSpace<T>, int, int) - Constructor for class edu.stanford.math.plex4.metric.landmark.MaxMinLandmarkSelector: This constructor initializes the landmark selector with a finite metric space, and a size parameter.
maxProbability - Variable in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
maxR - Variable in class edu.stanford.math.plex.LazyWitnessStream
maxR - Variable in class edu.stanford.math.plex.WitnessStream
maxS() - Method in class edu.stanford.math.plex.Chain: Return the largest basis element.
MaxSimplicialFilterFunction - Class in edu.stanford.math.plex4.streams.filter
MaxSimplicialFilterFunction(IntFilterFunction) - Constructor for class edu.stanford.math.plex4.streams.filter.MaxSimplicialFilterFunction
MED_PRECISION - Static variable in class edu.stanford.math.plex4.utility.ComparisonUtility
MemoryUtility - Class in edu.stanford.math.plex4.utility
MemoryUtility() - Constructor for class edu.stanford.math.plex4.utility.MemoryUtility
mergeBasisElts(Simplex[], int[], Simplex[], int[], int) - Method in class edu.stanford.math.plex.Chain
mergeDistances - Variable in class edu.stanford.math.clustering.HierarchicalClustering
mergeDistances - Variable in class edu.stanford.math.clustering.LinkageTree
mergedPairs - Variable in class edu.stanford.math.clustering.HierarchicalClustering
mergePairs - Variable in class edu.stanford.math.clustering.LinkageTree
message(String) - Method in class edu.stanford.math.plex.ExplicitStream
message(String) - Method in class edu.stanford.math.plex.PlexMessageWindow: Print a message string in the window.
message_window - Variable in class edu.stanford.math.plex.ExplicitStream
messageWindow(String) - Static method in class edu.stanford.math.plex.Plex: Make a Plex message window.
metricSpace - Variable in class edu.stanford.math.clustering.HierarchicalClustering
metricSpace - Variable in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
metricSpace - Variable in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector: This is the underlying metric space upon which the landmark set is build.
metricSpace - Variable in class edu.stanford.math.plex4.streams.impl.FlexibleVietorisRipsStream: This is the metric space upon which the stream is built from.
metricSpace - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream: This is the metric space upon which the stream is built from.
metricSpace - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream: This is the metric space upon which the stream is built from.
MetricUtility - Class in edu.stanford.math.mapper
MetricUtility() - Constructor for class edu.stanford.math.mapper.MetricUtility
MetricUtility - Class in edu.stanford.math.plex4.metric.utility: This class contains various functions for dealing with metric spaces.
MetricUtility() - Constructor for class edu.stanford.math.plex4.metric.utility.MetricUtility
minDimension - Variable in class edu.stanford.math.plex4.autogen.homology.BooleanPersistenceAlgorithm: This stores the minimum dimension for which to compute (co)homology.
minDimension - Variable in class edu.stanford.math.plex4.autogen.homology.IntPersistenceAlgorithm: This stores the minimum dimension for which to compute (co)homology.
minDimension - Variable in class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This stores the minimum dimension for which to compute (co)homology.
minDimension - Variable in class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This stores the minimum dimension for which to compute (co)homology.
minDimension - Variable in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
minDimension - Variable in class edu.stanford.math.plex4.homology.zigzag.ZigZagHomology: This stores the minimum dimension for which to compute (co)homology.
minLog2(int) - Static method in class edu.stanford.math.plex4.utility.MathUtility
minPositivePosition(int[]) - Static method in class edu.stanford.math.plex4.graph.random.PrescribedDegrees: Returns the first index of the smallest positive element or -1 if there are no positive entries
MinSimplicialFilterFunction - Class in edu.stanford.math.plex4.streams.filter
MinSimplicialFilterFunction(IntFilterFunction) - Constructor for class edu.stanford.math.plex4.streams.filter.MinSimplicialFilterFunction
minValue(List<ObjectIntPair<T>>) - Method in class edu.stanford.math.plex4.bottleneck.FlowNetwork
modularInverses(int) - Static method in class edu.stanford.math.plex4.utility.MathUtility: This function returns the multiplicative inverses of the integers [0, 1, ..., p-1] in mod p arithmetic.
mouseDragged() - Method in class edu.stanford.math.plex4.visualization.PAppletSplitscreen
mousePressed() - Method in class edu.stanford.math.plex4.visualization.HomologyGeneratorVisualizer
mousePressed() - Method in class edu.stanford.math.plex4.visualization.PAppletSplitscreen: Rotate 3D image when mouse is dragged
mouseReleased() - Method in class edu.stanford.math.plex4.visualization.PAppletSplitscreen
mParam - Variable in class edu.stanford.math.plex4.graph.random.BAGraph
multiMinus(int[], int, int) - Method in class edu.stanford.math.plex4.graph.random.PrescribedDegrees: Returns the array ds with 1 subtracted from the i-th element and 1 subtracted from the j-th element.
multiplicative_inverses(int) - Static method in class edu.stanford.math.plex.PersistenceBasis
multiply(Map<X, IntSparseFormalSum<Y>>, IntSparseFormalSum<X>, IntAbstractField) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function performs matrix multiplication.
multiply(Map<X, IntSparseFormalSum<Y>>, Map<Z, IntSparseFormalSum<X>>, IntAbstractField) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility: This function performs matrix-matrix multiplication.

N

N - Variable in class edu.stanford.math.plex.DiscreteSpace
N - Variable in class edu.stanford.math.plex.PointData.Discrete
N - Variable in class edu.stanford.math.plex.SimplexFaceIterator
n - Variable in class edu.stanford.math.plex4.graph.random.BinaryTree
n - Variable in class edu.stanford.math.plex4.graph.random.BinaryTreeGraph
n - Variable in class edu.stanford.math.plex4.graph.random.ErdosRenyiGraph
n - Variable in class edu.stanford.math.plex4.graph.random.StochasticBlockmodel
N - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
N - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream
name - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonNode
nearestNeighborSearch(double[]) - Method in class edu.stanford.math.plex4.kd.KDTree: This function returns the index of the nearest neighbor to the query point.
neighborhoodGraph - Variable in class edu.stanford.math.plex4.streams.impl.FlagComplexStream: Stores the neighborhood graph.
newLine() - Method in class edu.stanford.math.plex4.io.MatlabWriter: This function outputs a new line to the file.
newPlotWindow() - Method in class edu.stanford.math.plex4.io.MatlabWriter
next() - Method in class edu.stanford.math.plex.Cone
next() - Method in class edu.stanford.math.plex.ExplicitStream.DComplex: Return a DComplex of the next largest dimension, if there is one, else null.
next() - Method in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator: Returns the next Simplex in the iteration of the stream.
next() - Method in class edu.stanford.math.plex.ExplicitStream: Next Simplex in the stream.
next() - Method in class edu.stanford.math.plex.LazyWitnessStream: Next Simplex in the stream.
next() - Method in class edu.stanford.math.plex.PointData.Discrete.DSS
next() - Method in class edu.stanford.math.plex.RipsStream: Next Simplex in the stream.
next() - Method in class edu.stanford.math.plex.SimplexFaceIterator: Get the next face in an iteration of all faces of dimension k.
next() - Method in class edu.stanford.math.plex.SimplexStream: Next Simplex in the stream.
next() - Method in class edu.stanford.math.plex.SimplexStream.Stack: Return the next Simplex in the stream.
next - Variable in class edu.stanford.math.plex.SimplexStream.Stack.Segment
next() - Method in class edu.stanford.math.plex.SimplexStream.Stack.StackIterator: Returns the next Simplex in the iteration of the Stack.
next() - Method in class edu.stanford.math.plex.SimplexTable.SimpleTableIterator: Returns the next Simplex in the iteration over the table.
next() - Method in class edu.stanford.math.plex.TmpStream: Returns the next Simplex in the iteration of the Stack.
next() - Method in class edu.stanford.math.plex.WitnessStream: Next Simplex in the stream.
next() - Method in class edu.stanford.math.plex4.graph.UndirectedListEdgeIterator
next() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructureIterator
next() - Method in class edu.stanford.math.plex4.streams.storage_structures.IntOrderedIterator
nextBernoulli(double) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function returns a sample of a Bernoulli random variable with parameter p.
nextEntry() - Method in class edu.stanford.math.plex.SimplexStream.Head: Get the next entry from the underlying Queue.
nextNormal() - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function returns a normal random number.
nextUniform() - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function returns a uniform random number in the open interval (0, 1).
nextUniformInt(int, int) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: Returns a uniformly distributed integer in the inclusive interval {from, ..., to}
nextUniformIntExcluded(int, int, int) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function returns an integer uniformly distributed in the set {from, ..., to} \ {exclusion}.
nodeCount - Variable in class edu.stanford.math.plex4.graph.random.ForestFireGraph
normalArray(int, boolean) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function returns an array of normally distributed random numbers.
normalArray(int) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function returns an array of normally distributed random numbers.
normalize(Simplex[], int[], int) - Static method in class edu.stanford.math.plex.Chain
normalizeUpperBound(double) - Static method in class edu.stanford.math.plex.Plex
normalMatrix(int, int) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function returns a matrix containing normally distributed random numbers.
nParam - Variable in class edu.stanford.math.plex4.graph.random.BAGraph
nu - Variable in class edu.stanford.math.plex.LazyWitnessStream
nu - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream: This is the nu value described in the paper.
num_pts - Variable in class edu.stanford.math.plex.PointData.Discrete.DSS
numbers - Variable in class edu.stanford.math.plex.Plex.BettiNumbers
numBins - Variable in class edu.stanford.math.mapper.HistogramCreator
numColumns - Variable in class edu.stanford.math.plex4.io.Table
numNeighbors - Variable in class edu.stanford.math.plex4.graph.random.CircleGraph
numNodes - Variable in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
numNodes - Variable in class edu.stanford.math.plex4.graph.random.CircleGraph
numNodes - Variable in class edu.stanford.math.plex4.graph.random.PrescribedDegrees
numNodes - Variable in class edu.stanford.math.plex4.graph.random.RandomGeometricGraph
numRewired - Variable in class edu.stanford.math.plex4.graph.random.CircleGraph
numRows - Variable in class edu.stanford.math.plex4.io.Table

O

ObjectAbsoluteHomology<F,U> - Class in edu.stanford.math.plex4.autogen.homology
ObjectAbsoluteHomology(ObjectAbstractField<F>, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.ObjectAbsoluteHomology: This constructor initializes the object with a field and a comparator on the basis type.
ObjectClassicalHomology<F,U> - Class in edu.stanford.math.plex4.autogen.homology: This class performs the persistent homology algorithm as outlined in the paper "Computing Persistent Homology" by Zomorodian and Carlsson.
ObjectClassicalHomology(ObjectAbstractField<F>, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.ObjectClassicalHomology: This constructor initializes the object with a field and a comparator on the basis type.
objectIndexMap - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
objectIndexMap - Variable in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
ObjectPersistenceAlgorithm<F,U> - Class in edu.stanford.math.plex4.autogen.homology: This class defines the functionality for a persistence algorithm with underlying field type being F and underlying basis element type being U.
ObjectPersistenceAlgorithm(ObjectAbstractField<F>, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.ObjectPersistenceAlgorithm: This constructor initializes the object with a field and a comparator on the basis type.
ObjectPersistentHomology<F,U> - Class in edu.stanford.math.plex4.autogen.homology: This class defines the functionality for a persistence algorithm with underlying field type being F and underlying basis element type being U.
ObjectPersistentHomology(ObjectAbstractField<F>, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.ObjectPersistentHomology: This constructor initializes the object with a field and a comparator on the basis type.
ObjectReader<T> - Interface in edu.stanford.math.plex4.io
ObjectRelativeHomology<F,U> - Class in edu.stanford.math.plex4.autogen.homology
ObjectRelativeHomology(ObjectAbstractField<F>, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.autogen.homology.ObjectRelativeHomology: This constructor initializes the object with a field and a comparator on the basis type.
ObjectSearchableFiniteMetricSpace<T> - Class in edu.stanford.math.plex4.metric.impl: This class implements the AbstractSearchableMetricSpace interface over type T.
ObjectSearchableFiniteMetricSpace(T[]) - Constructor for class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace: This constructor initializes the class with an array of elements.
ObjectWriter<T> - Interface in edu.stanford.math.plex4.io
ObjReader - Class in edu.stanford.math.plex4.io
ObjReader() - Constructor for class edu.stanford.math.plex4.io.ObjReader
ON_BOTTOM - Static variable in class edu.stanford.math.plex.BCPlot.DrawingPane
ON_LEFT - Static variable in class edu.stanford.math.plex.BCPlot.DrawingPane
ON_RIGHT - Static variable in class edu.stanford.math.plex.BCPlot.DrawingPane
ON_TOP - Static variable in class edu.stanford.math.plex.BCPlot.DrawingPane
open() - Method in class edu.stanford.math.plex.ExplicitStream
open_count - Variable in class edu.stanford.math.plex.ExplicitStream.DComplex
open_count - Variable in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
open_count - Variable in class edu.stanford.math.plex.ExplicitStream
openIntervals - Variable in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker

P

p - Static variable in class edu.stanford.math.plex.PersistenceBasis
p - Variable in class edu.stanford.math.plex4.graph.random.ErdosRenyiGraph
p6_v_to_l_hi(int[]) - Static method in class edu.stanford.math.plex.Packed6Simplex
p6_v_to_l_lo(int[]) - Static method in class edu.stanford.math.plex.Packed6Simplex
p6_v_to_l_mid(int[]) - Static method in class edu.stanford.math.plex.Packed6Simplex
p8_v_to_l_hi(int[]) - Static method in class edu.stanford.math.plex.Packed8Simplex
p8_v_to_l_hi_mid(int[]) - Static method in class edu.stanford.math.plex.Packed8Simplex
p8_v_to_l_lo(int[]) - Static method in class edu.stanford.math.plex.Packed8Simplex
p8_v_to_l_lo_mid(int[]) - Static method in class edu.stanford.math.plex.Packed8Simplex
p_edge - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonNode
p_max - Variable in class edu.stanford.math.plex.RDirectBufferData: Max number of points.
Packed2Simplex - Class in edu.stanford.math.plex: The Packed2Simplex class implements the abstract class Simplex for Simplices that are points or edges by storing the vertices as 2 packed 32-bit values in a single long int.
Packed2Simplex() - Constructor for class edu.stanford.math.plex.Packed2Simplex
Packed2Simplex(long) - Constructor for class edu.stanford.math.plex.Packed2Simplex
Packed2Simplex(int) - Constructor for class edu.stanford.math.plex.Packed2Simplex
Packed4Simplex - Class in edu.stanford.math.plex: The Packed4Simplex class implements the abstract class Simplex for Simplices of dimension at most 3 by storing the vertices as 4 packed positive integer values in a pair of long ints.
Packed4Simplex() - Constructor for class edu.stanford.math.plex.Packed4Simplex
Packed4Simplex(long, long) - Constructor for class edu.stanford.math.plex.Packed4Simplex
Packed4Simplex(int, int, int) - Constructor for class edu.stanford.math.plex.Packed4Simplex
Packed6Simplex - Class in edu.stanford.math.plex: The Packed6Simplex class implements the abstract class Simplex for Simplices of dimension 4-5 by storing the vertices as 6 packed positive integer values in three long integers.
Packed6Simplex() - Constructor for class edu.stanford.math.plex.Packed6Simplex
Packed6Simplex(long, long, long) - Constructor for class edu.stanford.math.plex.Packed6Simplex
Packed8Simplex - Class in edu.stanford.math.plex: The Packed8Simplex class implements the abstract class Simplex for Simplices of dimension 6-7 by storing the vertices as 8 packed positive integer values in three long integers.
Packed8Simplex() - Constructor for class edu.stanford.math.plex.Packed8Simplex
Packed8Simplex(long, long, long, long) - Constructor for class edu.stanford.math.plex.Packed8Simplex
Packed8Simplex(int, int, int, int, int, int, int) - Constructor for class edu.stanford.math.plex.Packed8Simplex
Packed8Simplex(int, int, int, int, int, int, int, int) - Constructor for class edu.stanford.math.plex.Packed8Simplex
paintComponent(Graphics) - Method in class edu.stanford.math.plex.BCPlot.DrawingPane
paintComponent(Graphics) - Method in class edu.stanford.math.plex.BCPlot.Ruler
PaperTestCase() - Static method in class edu.stanford.math.plex.TmpStream
PAppletSplitscreen - Class in edu.stanford.math.plex4.visualization
PAppletSplitscreen() - Constructor for class edu.stanford.math.plex4.visualization.PAppletSplitscreen
parameters_table - Variable in class edu.stanford.math.plex.ExplicitStream
parent - Variable in class edu.stanford.math.plex.ExplicitStream.DComplex
parent() - Method in class edu.stanford.math.plex.ExplicitStream.DComplex: Return the parent ExplicitStream of this DComplex.
parent - Variable in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
parent - Variable in class edu.stanford.math.plex.SimplexTable.SimpleTableIterator
parent_is_consistent() - Method in class edu.stanford.math.plex.ExplicitStream.DComplex
parent_is_consistent() - Method in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
parent_is_consistent() - Method in class edu.stanford.math.plex.SimplexTable.SimpleTableIterator
parents - Variable in class edu.stanford.math.clustering.DisjointSetSystem
partition(T[], int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericArray: The fundamental partition operation for quicksort.
partition(List<T>, int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericList
partition(int[], int, int) - Static method in class edu.stanford.math.plex4.utility.Quicksort.Int: The fundamental partition operation for quicksort.
pdata - Variable in class edu.stanford.math.plex.LazyWitnessStream
pdata - Variable in class edu.stanford.math.plex.RipsStream: The PointData underlying this Rips complex.
pdata - Variable in class edu.stanford.math.plex.WitnessStream
performBinning() - Method in class edu.stanford.math.mapper.HistogramCreator
performBootstrap() - Method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.VietorisRipsBootstrapper
performClustering() - Method in class edu.stanford.math.clustering.HierarchicalClustering
performClustering() - Method in class edu.stanford.math.clustering.SingleLinkageClustering
performGaussianKernelDensityEstimation(AbstractIntMetricSpace, double) - Static method in class edu.stanford.math.plex4.metric.utility.DensityEstimation
performProjectionBootstrap() - Method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
performProjectionBootstrap(int[]) - Method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
permute(int[]) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function computes a random permutation of the input array, and then applies the permutation.
Persistence - Class in edu.stanford.math.plex: The Persistence class class implements the algorithm of Zomorodian and Carlsson for computing the persistent homology groups with coefficients in a finite field.
Persistence() - Constructor for class edu.stanford.math.plex.Persistence
Persistence() - Static method in class edu.stanford.math.plex.Plex: Create a Persistence instance.
persistence_parameters - Variable in class edu.stanford.math.plex.ExplicitStream
persistence_sort(Simplex[]) - Static method in class edu.stanford.math.plex.Simplex: Sort, in place and using "persistence order", an array of simplices.
PersistenceAlgorithmInterface - Class in edu.stanford.math.plex4.api
PersistenceAlgorithmInterface() - Constructor for class edu.stanford.math.plex4.api.PersistenceAlgorithmInterface
PersistenceBasis - Class in edu.stanford.math.plex: The class PersistenceBasis implements the Persistence algorithm by Carlsson-Zomorodian, with additional basis element tracking to make sure that afterwards, basis elements for the persistence intervals may be extracted.
PersistenceBasis() - Constructor for class edu.stanford.math.plex.PersistenceBasis
PersistenceBasis() - Static method in class edu.stanford.math.plex.Plex: Create a PersistenceBasis instance.
PersistenceBasis.ListItem - Class in edu.stanford.math.plex
PersistenceBasis.ListItem() - Constructor for class edu.stanford.math.plex.PersistenceBasis.ListItem
PersistenceBasis.SimplexType - Enum in edu.stanford.math.plex
PersistenceBasisInterval - Class in edu.stanford.math.plex: PersistenceBasisInterval instances encode a dimension and a duration (e.g., start and end times) as well as a basis element for each interval.
PersistenceBasisInterval(int) - Constructor for class edu.stanford.math.plex.PersistenceBasisInterval
PersistenceBasisInterval.Float - Class in edu.stanford.math.plex
PersistenceBasisInterval.Float() - Constructor for class edu.stanford.math.plex.PersistenceBasisInterval.Float
PersistenceBasisInterval.Float(Chain, double, double) - Constructor for class edu.stanford.math.plex.PersistenceBasisInterval.Float
PersistenceBasisInterval.Float(Chain, double) - Constructor for class edu.stanford.math.plex.PersistenceBasisInterval.Float
PersistenceBasisInterval.Int - Class in edu.stanford.math.plex
PersistenceBasisInterval.Int() - Constructor for class edu.stanford.math.plex.PersistenceBasisInterval.Int
PersistenceBasisInterval.Int(Chain, int, int) - Constructor for class edu.stanford.math.plex.PersistenceBasisInterval.Int
PersistenceBasisInterval.Int(Chain, int) - Constructor for class edu.stanford.math.plex.PersistenceBasisInterval.Int
PersistenceInterval - Class in edu.stanford.math.plex: PersistenceInterval instances encode a dimension and a duration (e.g., start and end times).
PersistenceInterval.Float - Class in edu.stanford.math.plex
PersistenceInterval.Float(int, double, double) - Constructor for class edu.stanford.math.plex.PersistenceInterval.Float
PersistenceInterval.Float(int, double) - Constructor for class edu.stanford.math.plex.PersistenceInterval.Float
PersistenceInterval.Int - Class in edu.stanford.math.plex
PersistenceInterval.Int(int, int, int) - Constructor for class edu.stanford.math.plex.PersistenceInterval.Int
PersistenceInterval.Int(int, int) - Constructor for class edu.stanford.math.plex.PersistenceInterval.Int
PersistenceInvariantDescriptor<I,G> - Class in edu.stanford.math.plex4.homology.barcodes: This class is designed to store persistence algorithm invariants for each dimension, with additional information about the generators.
PersistenceInvariantDescriptor() - Constructor for class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor
PersistentCohomologyPrototype - Class in edu.stanford.math.plex4.homology.nonautogen
PersistentCohomologyPrototype(IntAbstractField, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.homology.nonautogen.PersistentCohomologyPrototype: This constructor initializes the object with a field and a comparator on the basis type.
pInverses - Static variable in class edu.stanford.math.plex.PersistenceBasis
pixelsPerUnit - Variable in class edu.stanford.math.plex.BCPlot
Plex - Class in edu.stanford.math.plex: The Plex class provides some utility functions that don't have a clearly defined home, and some entry points into plex library code that are especially useful when in matlab.
Plex() - Constructor for class edu.stanford.math.plex.Plex
Plex.BettiNumbers - Class in edu.stanford.math.plex: An array of Betti numbers (int[]) boxed up for convenience.
Plex.BettiNumbers() - Constructor for class edu.stanford.math.plex.Plex.BettiNumbers
Plex.BettiNumbers(int[]) - Constructor for class edu.stanford.math.plex.Plex.BettiNumbers: Encapsulate a verified array of Betti numbers.
plex3Compatible - Variable in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
plex3Compatible - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream
Plex3PersistenceAlgorithm - Class in edu.stanford.math.plex4.interop: This class encapsulates the functionality of the original version of javaPlex.
Plex3PersistenceAlgorithm(int) - Constructor for class edu.stanford.math.plex4.interop.Plex3PersistenceAlgorithm: This constructor initializes the class with the maximum dimension to compute persistence for.
Plex3Stream - Class in edu.stanford.math.plex4.interop: This class is a wrapper around a plex 3 SimplexStream that implements the AbstractFilteredStream interface of plex 4.
Plex3Stream(SimplexStream) - Constructor for class edu.stanford.math.plex4.interop.Plex3Stream
Plex3Stream(SimplexStream, int[]) - Constructor for class edu.stanford.math.plex4.interop.Plex3Stream
Plex3ToPlex4BarcodeAdapter - Class in edu.stanford.math.plex4.interop: This class implements a function object which converts plex 3 barcodes to plex 4 barcodes.
Plex3ToPlex4SimplexAdapter - Class in edu.stanford.math.plex4.interop: This class implements a function object which converts plex 3 simplices to plex 4 simplices.
Plex4 - Class in edu.stanford.math.plex4.api: This class contains static functions that are designed to be callable from Matlab.
Plex4() - Constructor for class edu.stanford.math.plex4.api.Plex4
PlexInterpreter - Class in bsh: The PlexInterpreter class is a wrapper for Interpreter whose only purpose at the moment is to allow users to log their input to a file.
PlexInterpreter(ConsoleInterface, String) - Constructor for class bsh.PlexInterpreter: Constructor PlexInterpreter, only called in the makeWorkspace.bsh script.
PlexInterpreter(String) - Constructor for class bsh.PlexInterpreter: Constructor PlexInterpreter, only called in the makeListener.bsh.
PlexMessageWindow - Class in edu.stanford.math.plex: A PlexMessageWindow instance is a scrollable text window in which we can insert messages.
PlexMessageWindow(String) - Constructor for class edu.stanford.math.plex.PlexMessageWindow: Create a new PlexMessageWindow with the given title.
PlexReader - Class in bsh: The PlexReader class is a wrapper for the input Reader for interactive Interpreter instances.
PlexReader(Reader, String) - Constructor for class bsh.PlexReader: Constructor PlexReader, only called by PlexInterpreter().
PlexSort - Class in edu.stanford.math.plex: The PlexSort class provides a sorting routine that I'd prefer was part of the standard libraries.
PlexSort() - Constructor for class edu.stanford.math.plex.PlexSort
PlexSort.Comp - Class in edu.stanford.math.plex: Instances of the Comp inner class are used as comparison closures for the sorting routine comp_sort.
PlexSort.Comp() - Constructor for class edu.stanford.math.plex.PlexSort.Comp
PlexSort.CompL - Class in edu.stanford.math.plex
PlexSort.CompL() - Constructor for class edu.stanford.math.plex.PlexSort.CompL
PlexSort.CompObj - Class in edu.stanford.math.plex
PlexSort.CompObj() - Constructor for class edu.stanford.math.plex.PlexSort.CompObj
plot(String, double[][], double, boolean) - Static method in class edu.stanford.math.plex.BCPlot: Create the plot window and display results.
plot(PersistenceInterval[], String, double) - Static method in class edu.stanford.math.plex.Plex: Plot an array of Plex barcodes (that is, a PersistenceInterval[]).
plot(PersistenceBasisInterval[], String, double) - Static method in class edu.stanford.math.plex.Plex: Plot an array of Plex barcodes computed with bases.
plotBeingSaved - Variable in class edu.stanford.math.plex.BCPlot
plotTypeScatter - Variable in class edu.stanford.math.plex.BCPlot
plotUpperBound - Variable in class edu.stanford.math.plex.BCPlot
plotValue - Variable in class edu.stanford.math.plex.BCPlot
Point2D - Class in edu.stanford.math.plex4.visualization
Point2D(float, float) - Constructor for class edu.stanford.math.plex4.visualization.Point2D
PointCloudExamples - Class in edu.stanford.math.plex4.examples: This static class contains various functions which produce examples of point cloud data sets.
PointCloudExamples() - Constructor for class edu.stanford.math.plex4.examples.PointCloudExamples
PointCloudScaling - Class in edu.stanford.math.plex4.visualization
PointCloudScaling() - Constructor for class edu.stanford.math.plex4.visualization.PointCloudScaling
PointData - Class in edu.stanford.math.plex: A PointData instance encodes distance information for a data set.
PointData() - Constructor for class edu.stanford.math.plex.PointData
PointData.Discrete - Class in edu.stanford.math.plex
PointData.Discrete() - Constructor for class edu.stanford.math.plex.PointData.Discrete
PointData.Discrete(int) - Constructor for class edu.stanford.math.plex.PointData.Discrete: Make a PointData.Discrete with N points.
PointData.Discrete.DSS - Class in edu.stanford.math.plex
PointData.Discrete.DSS() - Constructor for class edu.stanford.math.plex.PointData.Discrete.DSS
PointData.Discrete.DSS(SimplexStream, int, int) - Constructor for class edu.stanford.math.plex.PointData.Discrete.DSS
PointData.NSpace - Class in edu.stanford.math.plex: NSpace instances also provide dimension information.
PointData.NSpace() - Constructor for class edu.stanford.math.plex.PointData.NSpace
PointData.Predicate - Class in edu.stanford.math.plex: Predicate instances are used weed out points that are uninteresting in a given context (e.g., density too low or high).
PointData.Predicate() - Constructor for class edu.stanford.math.plex.PointData.Predicate
points - Variable in class edu.stanford.math.plex4.graph.random.ManifoldGraph
pointsAreConsistent(double[], int) - Method in class edu.stanford.math.plex.EuclideanArrayData
pointsAreConsistent(double[][]) - Method in class edu.stanford.math.plex.EuclideanArrayData
prependColumn(Map<Integer, X>, X) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
PrescribedDegrees - Class in edu.stanford.math.plex4.graph.random: Implements a random prescribed degree graph by the algorithm presented in J.Blitstein and P.Diaconis
PrescribedDegrees(int[]) - Constructor for class edu.stanford.math.plex4.graph.random.PrescribedDegrees
prev - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonNode
PrimitiveBasisElement - Interface in edu.stanford.math.plex4.homology.chain_basis: This interface defines the functionality of a primitive basis element type for a chain complex.
PrimitiveMultifilteredStream<T extends PrimitiveBasisElement> - Class in edu.stanford.math.plex4.streams.multi
PrimitiveMultifilteredStream() - Constructor for class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
PrimitiveStream<T extends PrimitiveBasisElement> - Class in edu.stanford.math.plex4.streams.interfaces: This class implements a filtered chain complex where the underlying type is a geometric primitive (a Simplex or a Cell).
PrimitiveStream(StreamStorageStructure<T>) - Constructor for class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream: This constructor constructs the stream with the supplied StreamStorageStructure.
PrimitiveStream(Comparator<T>) - Constructor for class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream: This constructor construct the stream with the default storage scheme.
printable_intervals(PersistenceInterval[]) - Static method in class edu.stanford.math.plex.Plex
probabilityMatrix - Variable in class edu.stanford.math.plex4.graph.random.StochasticBlockmodel
producePartialClustering(IntFilterFunction, AbstractIntMetricSpace, MapperSpecifier) - Static method in class edu.stanford.math.mapper.MapperPipeline
project(AbstractHomologyTracker<Integer, I, ?, IntSparseFormalSum>, AbstractHomologyTracker<Integer, I, ?, IntSparseFormalSum<V>>, AbstractHomologyTracker<Integer, I, ?, IntSparseFormalSum>, AbstractPersistenceTracker<Integer, I, IntSparseFormalSum>, IntAlgebraicFreeModule, IntAlgebraicFreeModule<V>, I, I) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.InducedHomologyMappingUtility
projectFirst(IntSparseFormalSum<? extends ObjectObjectPair<U, U>>, IntAlgebraicFreeModule) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.SimplexStreamUtility
projectSecond(IntSparseFormalSum<? extends ObjectObjectPair<U, U>>, IntAlgebraicFreeModule) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.SimplexStreamUtility
prune(int[]) - Method in class edu.stanford.math.plex.ExplicitStream: Remove a simplex, specified by its vertex vector, and any simplex that contains it, from the stream.
prune(double[]) - Method in class edu.stanford.math.plex.ExplicitStream: Prune a simplex, specified by an array of double, from the stream.
prune(int[][]) - Method in class edu.stanford.math.plex.ExplicitStream: Prune an array of simplices, specified by vertex vectors, from the stream.
prune(double[][]) - Method in class edu.stanford.math.plex.ExplicitStream: Prune an array of simplices, specified by double[] vertex vectors, from the stream.
ptArrayIsSubset(int[], int[]) - Static method in class edu.stanford.math.plex.Plex
pullUpIndices(TIntHashSet, TIntHashSet) - Static method in class edu.stanford.math.mapper.MapperPipeline
push(Simplex) - Method in class edu.stanford.math.plex.SimplexStream.Stack: Push a Simplex into the stream.
push(Simplex) - Method in class edu.stanford.math.plex.SimplexStream.Stack.Segment
put(Simplex) - Method in class edu.stanford.math.plex.SimplexTable: Intern a Simplex.

Q

Quicksort - Class in edu.stanford.math.plex4.utility: This class contains an implement of the quicksort and other related algorithms, such as the selection of order statistics.
quicksort(T[], Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericArray: Performs the quicksort algorithm in place on the supplied array.
quicksort(T[], int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericArray: Performs the quicksort algorithm in place on a subarray of the supplied array.
quicksort(List<T>, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericList
quicksort(List<T>, int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericList
quicksort(int[]) - Static method in class edu.stanford.math.plex4.utility.Quicksort.Int: Performs the quicksort algorithm in place on the supplied array.
quicksort(int[], int, int) - Static method in class edu.stanford.math.plex4.utility.Quicksort.Int: Performs the quicksort algorithm in place on a subarray of the supplied array.
Quicksort.GenericArray<T> - Class in edu.stanford.math.plex4.utility
Quicksort.GenericArray() - Constructor for class edu.stanford.math.plex4.utility.Quicksort.GenericArray
Quicksort.GenericList<T> - Class in edu.stanford.math.plex4.utility
Quicksort.GenericList() - Constructor for class edu.stanford.math.plex4.utility.Quicksort.GenericList
Quicksort.Int - Class in edu.stanford.math.plex4.utility
Quicksort.Int() - Constructor for class edu.stanford.math.plex4.utility.Quicksort.Int

R

rand - Static variable in class edu.stanford.math.plex.Plex
rand - Static variable in class edu.stanford.math.plex.PointData
random_index_subset(int, int[], int) - Static method in class edu.stanford.math.plex.Plex: Take subset_size distinct entries from the integers 0 through N-1, and put them in the initial segment of subset[].
random_permutation(int[]) - Static method in class edu.stanford.math.plex.Plex: Make a random permutation of the integers 0 through perm.length-1 and put them in perm.
random_points(int) - Method in class edu.stanford.math.plex.PointData: Return a sorted array of distinct indices for "random points" in the metric space.
random_subset(int[], int, int[], int) - Static method in class edu.stanford.math.plex.Plex: Take subset_size distinct entries from initial segment of length set_size in set[] and put them in the initial segment of subset[].
random_subset(int[], int[]) - Static method in class edu.stanford.math.plex.Plex: Take subset.length distinct entries from set[], and put them in subset[].
random_subset(int, int[], int) - Static method in class edu.stanford.math.plex.Plex: Take subset_size distinct entries from the integers 1 through N, and put them in the initial segment of subset[].
random_subset(int, int[]) - Static method in class edu.stanford.math.plex.Plex: Take subset.length distinct entries from the integers 1 through N, and put them in subset[].
randomEngine - Variable in class edu.stanford.math.plex4.graph.random.ForestFireGraph
RandomGeometricGraph - Class in edu.stanford.math.plex4.graph.random: Generates n random points in [0,1]^d and connects an edge between points x and y if d(x,y)
RandomGeometricGraph(int, int, double) - Constructor for class edu.stanford.math.plex4.graph.random.RandomGeometricGraph
randomizedPartition(T[], int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericArray: This function performs the same function as the partition function, except that it uses a randomly chosen pivot.
randomizedPartition(List<T>, int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericList
randomizedPartition(int[], int, int) - Static method in class edu.stanford.math.plex4.utility.Quicksort.Int: This function performs the same function as the partition function, except that it uses a randomly chosen pivot.
randomizedQuicksort(T[], Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericArray: This performs the randomized quicksort algorithm in place on the supplied array.
randomizedQuicksort(T[], int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericArray: This performs the randomized quicksort algorithm in place on a subarray of the supplied array.
randomizedQuicksort(List<T>, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericList: This performs the randomized quicksort algorithm in place on the supplied array.
randomizedQuicksort(List<T>, int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericList: This performs the randomized quicksort algorithm in place on a subarray of the supplied array.
randomizedQuicksort(int[]) - Static method in class edu.stanford.math.plex4.utility.Quicksort.Int: This performs the randomized quicksort algorithm in place on the supplied array.
randomizedQuicksort(int[], int, int) - Static method in class edu.stanford.math.plex4.utility.Quicksort.Int: This performs the randomized quicksort algorithm in place on a subarray of the supplied array.
randomizedSelect(T[], int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericArray: This function returns the i-th order statistic of the data in the supplied array.
randomizedSelect(T[], int, int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericArray: This function performs the randomizedSelect on a subarray of the supplied array.
randomizedSelect(List<T>, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericList
randomizedSelect(List<T>, int, int, int, Comparator<T>) - Static method in class edu.stanford.math.plex4.utility.Quicksort.GenericList
randomizedSelect(int[], int) - Static method in class edu.stanford.math.plex4.utility.Quicksort.Int: This function returns the i-th order statistic of the data in the supplied array.
randomizedSelect(int[], int, int, int) - Static method in class edu.stanford.math.plex4.utility.Quicksort.Int: This function performs the randomizedSelect on a subarray of the supplied array.
RandomLandmarkSelector<T> - Class in edu.stanford.math.plex4.metric.landmark: This class defines a landmark set in a finite metric space by random selection.
RandomLandmarkSelector(AbstractSearchableMetricSpace<T>, int) - Constructor for class edu.stanford.math.plex4.metric.landmark.RandomLandmarkSelector: This constructor initializes the landmark selector with a finite metric space, and a size parameter.
RandomProjectionFilterFunction - Class in edu.stanford.math.plex4.streams.filter
RandomProjectionFilterFunction(EuclideanMetricSpace) - Constructor for class edu.stanford.math.plex4.streams.filter.RandomProjectionFilterFunction
RandomProjectionFilterFunction(double[][]) - Constructor for class edu.stanford.math.plex4.streams.filter.RandomProjectionFilterFunction
randomSubset(int, int) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function computes a random subset of size subsetSize from the set {0, ..., selectionSetSize - 1}.
RandomUtility - Class in edu.stanford.math.plex4.utility: This class contains static members for generating random numbers.
RandomUtility() - Constructor for class edu.stanford.math.plex4.utility.RandomUtility
RangeCoverUtility - Class in edu.stanford.math.mapper
RangeCoverUtility() - Constructor for class edu.stanford.math.mapper.RangeCoverUtility
ranks - Variable in class edu.stanford.math.clustering.DisjointSetSystem
rdb() - Method in class edu.stanford.math.plex4.bottleneck.FordFulkerson
RDirectBufferData - Class in edu.stanford.math.plex: The RDirectBufferData is a mechanism for transforming an R distance matrix into a PointData.
RDirectBufferData(int, ByteBuffer) - Constructor for class edu.stanford.math.plex.RDirectBufferData: Use a pre-allocated buffer of doubles as the distance matrix.
read(char[], int, int) - Method in class bsh.PlexReader: Wrapper for normal read to buffer operation.
readCSVFile(String, String, boolean, boolean) - Static method in class edu.stanford.math.plex4.io.FileIOUtility: This function reads a CSV file and outputs the values into a Table object.
readMatrix(Reader) - Static method in class edu.stanford.math.plex.Plex: Read a double[][] from a stream.
readMatrix(String) - Static method in class edu.stanford.math.plex.Plex: Read a double[][] from a file.
readNumericCSVFile(String, String) - Static method in class edu.stanford.math.plex4.io.FileIOUtility
reduce(Map<X, IntSparseFormalSum<Y>>, IntSparseFormalSum<Y>, Comparator<Y>, IntAlgebraicFreeModule<Y>) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
remove() - Method in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator: Unsupported remove() operation.
remove(int[]) - Method in class edu.stanford.math.plex.ExplicitStream: Remove a simplex, specified by its vertex vector, from the stream.
remove(double[]) - Method in class edu.stanford.math.plex.ExplicitStream: Remove a simplex, specified by its vertex vector as an array of double, from the stream.
remove(int[][]) - Method in class edu.stanford.math.plex.ExplicitStream: Remove an array of simplices, specified by vertex vectors, from the stream.
remove(double[][]) - Method in class edu.stanford.math.plex.ExplicitStream: Remove an array of simplices, specified by double[] vertex vectors, from the stream.
remove() - Method in class edu.stanford.math.plex.SimplexStream: Unsupported remove() operation.
remove() - Method in class edu.stanford.math.plex.SimplexStream.Stack.StackIterator: Unsupported remove() operation.
remove() - Method in class edu.stanford.math.plex.SimplexTable.SimpleTableIterator: Unsupported remove() operation.
remove() - Method in class edu.stanford.math.plex.TmpStream: Unsupported remove() operation.
remove() - Method in class edu.stanford.math.plex4.graph.UndirectedListEdgeIterator
remove(U, K) - Method in interface edu.stanford.math.plex4.homology.zigzag.AbstractHomologyTracker
remove(U) - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
remove(U, int) - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
remove(U, Integer) - Method in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
remove(U, Integer) - Method in class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
remove() - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructureIterator: Currently we do not support removal from a hashed storage structure via an iterator.
remove() - Method in class edu.stanford.math.plex4.streams.storage_structures.IntOrderedIterator
removeEdge(int, int) - Method in interface edu.stanford.math.plex4.graph.AbstractUndirectedGraph: This function removes the edge (i, j) from the graph.
removeEdge(int, int) - Method in class edu.stanford.math.plex4.graph.UndirectedListGraph
removeEdge(int, int) - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
removeElement(T) - Method in class edu.stanford.math.plex4.streams.storage_structures.HashedStorageStructure
removeElement(T) - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
removeElement(T) - Method in interface edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructure: This function removes the specified element form the storage structure.
removeElementIfPresent(int[]) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitSimplexStream
removeElementIfPresent(T) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitStream: This function removes the specified element from the stream.
removeIndex(int[], int) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility: This function returns a new array which contains the same entries as the supplied array except that the element at the specified index has been removed and the proceeding elements have been shifted down by one.
repeatString(String, int) - Static method in class edu.stanford.math.mapper.HistogramCreator
resetView() - Method in class edu.stanford.math.plex4.visualization.PAppletSplitscreen: Reset the view angle and
reverse(Map<X, Y>) - Static method in class edu.stanford.math.plex4.homology.zigzag.bootstrap.InducedHomologyMappingUtility
reverse_sort(int[], int[]) - Static method in class edu.stanford.math.plex.PlexSort
reverse_sort(int[], double[]) - Static method in class edu.stanford.math.plex.PlexSort
rewiringProbability - Variable in class edu.stanford.math.plex4.graph.random.CircleGraph
rewriteModP(int) - Method in class edu.stanford.math.plex.Chain: Rewrite an element in Z/p from the representation in the interval [0,p) to the representation in (-p/2,p/2).
rightMargin - Variable in class edu.stanford.math.plex.BCPlot
RipsStream(double, int, double, PointData) - Static method in class edu.stanford.math.plex.Plex: Make a stream of the simplices in a Rips complex for given data set.
RipsStream - Class in edu.stanford.math.plex: A RipsStream instance is SimplexStream whose elements are the simplices of the Rips complex of a PointData instance.
RipsStream() - Constructor for class edu.stanford.math.plex.RipsStream
rndd_minus - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
rndd_plus - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
rootedGraphSize - Variable in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph
roundUpToPowerOf2(int) - Static method in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph
rows - Variable in class edu.stanford.math.plex4.io.Table

S

s_and_c_okay(Simplex[], int[], int) - Static method in class edu.stanford.math.plex.Chain
saveAssociatedSimplices - Variable in class edu.stanford.math.plex4.streams.impl.WitnessStream
saveImage(File, String) - Method in class edu.stanford.math.plex.BCPlot.DrawingPane
saveImage(BufferedImage, String) - Static method in class edu.stanford.math.plex4.io.FileIOUtility: Saves a BufferedImage stream in PNG format.
scaleCoordinates(double[][], float) - Static method in class edu.stanford.math.plex4.visualization.PointCloudScaling: Returns a scaled version of the point cloud.
scatter(PersistenceInterval[], String, double) - Static method in class edu.stanford.math.plex.Plex: Make a scatterplot of a PersistenceInterval[].
scatter(PersistenceBasisInterval[], String, double) - Static method in class edu.stanford.math.plex.Plex: Make a scatterplot of a PersistenceBasisInterval[].
scrollPane - Variable in class edu.stanford.math.plex.PlexMessageWindow
segment_length - Variable in class edu.stanford.math.plex.SimplexStream.Stack
segments - Variable in class edu.stanford.math.plex.SimplexStream.Stack
segments - Variable in class edu.stanford.math.plex.SimplexStream.Stack.StackIterator
segments_index - Variable in class edu.stanford.math.plex.SimplexStream.Stack
segments_index - Variable in class edu.stanford.math.plex.SimplexStream.Stack.StackIterator
serializeObject(Object, String) - Static method in class edu.stanford.math.plex4.io.FileIOUtility: Try to save an object for quick reloading later.
serialVersionUID - Static variable in class bsh.PlexInterpreter
serialVersionUID - Static variable in class edu.stanford.math.plex.BCPlot.DrawingPane
serialVersionUID - Static variable in class edu.stanford.math.plex.BCPlot.fileSaveMenuHandler
serialVersionUID - Static variable in class edu.stanford.math.plex.BCPlot.Ruler
serialVersionUID - Static variable in class edu.stanford.math.plex.BCPlot
set_coordinate(int, int, double) - Method in class edu.stanford.math.plex.MappedBufferData: Set coordinates.
set_pt(int, double[]) - Method in class edu.stanford.math.plex.MappedBufferData: Set point.
setBaseModulus(int) - Static method in class edu.stanford.math.plex.Persistence: Set or reset the coefficient field.
setBaseModulus(int) - Static method in class edu.stanford.math.plex.PersistenceBasis: Set or reset the coefficient field.
setCapacity(int) - Method in class edu.stanford.math.plex4.bottleneck.FlowEdge
setChain(Chain) - Method in class edu.stanford.math.plex.Simplex: Set the chain value, provided it hasn't already been set.
setColumnHeading(int, String) - Method in class edu.stanford.math.plex4.io.Table: This function sets the heading of the specified column.
SetCover1D - Class in edu.stanford.math.mapper: This class computes the pre-image of a cover of the codomain of a function.
SetCover1D(IntFilterFunction, Iterable<Interval<Double>>) - Constructor for class edu.stanford.math.mapper.SetCover1D
setDefaultDir(String) - Static method in class bsh.PlexReader: Set the default logging directory.
setDefaultFlag(boolean) - Static method in class bsh.PlexReader: Set the default logging flag.
setEquals(Collection<?>, Collection<?>) - Static method in class edu.stanford.math.plex4.utility.ComparisonUtility: This function returns true if two Collections define the same set; that is they contain the same elements.
setEquals(TIntHashSet, TIntHashSet) - Static method in class edu.stanford.math.plex4.utility.ComparisonUtility: This function returns true if the two sets of integers contain the same elements.
setfindex(int) - Method in class edu.stanford.math.plex.Simplex: Set the findex value, provided it hasn't already been done.
setImplementationType(GraphInstanceGenerator.ImplementationType) - Method in class edu.stanford.math.plex4.graph.random.GraphInstanceGenerator
setLeft(KDNode) - Method in class edu.stanford.math.plex4.kd.KDNode
setLeftClosedDefault(boolean) - Method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection: This function sets the property that determines whether the left endpoint of created intervals is closed or not.
setLogfile(String) - Method in class bsh.PlexInterpreter: Specify the name of the logfile.
setLogfile(String) - Method in class bsh.PlexReader: Force logstream to go to specified filename.
setLogging - Class in bsh.commands: Set the global defaults for input logging.
setLogging() - Constructor for class bsh.commands.setLogging
setMajorLegend(String) - Method in class edu.stanford.math.plex.BCPlot: Sets the Major Legend
setMaxDimension(int) - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
setPlex3Compatbility(boolean) - Method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
setPlex3Compatbility(boolean) - Method in class edu.stanford.math.plex4.streams.impl.WitnessStream
setReverseEdge(FlowEdge) - Method in class edu.stanford.math.plex4.bottleneck.FlowEdge
setRight(KDNode) - Method in class edu.stanford.math.plex4.kd.KDNode
setRightClosedDefault(boolean) - Method in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection: This function sets the property that determines whether the right endpoint of created intervals is closed or not.
setTitle(String) - Method in class edu.stanford.math.plex4.io.Table: This function sets the title of the table.
setup() - Method in class edu.stanford.math.plex4.visualization.PAppletSplitscreen
setUseLeftClosedIntervals(boolean) - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
setUseRightClosedIntervals(boolean) - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
ShortestPathMetric - Class in edu.stanford.math.plex4.graph.metric: This class produces a metric space that is defined by the shortest-path distance between vertices in a graph.
signOfLast - Variable in class edu.stanford.math.plex.SimplexFaceIterator
signum(long) - Static method in class edu.stanford.math.plex4.utility.MathUtility
signum(double) - Static method in class edu.stanford.math.plex4.utility.MathUtility
SimpleHomologyBasisTracker - Class in edu.stanford.math.plex4.homology.zigzag
SimpleHomologyBasisTracker(IntAbstractField, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.homology.zigzag.SimpleHomologyBasisTracker
Simplex - Class in edu.stanford.math.plex: A Simplex is the basic unit for simplicial homology calculations, literally.
Simplex() - Constructor for class edu.stanford.math.plex.Simplex
Simplex - Class in edu.stanford.math.plex4.homology.chain_basis: This class implements the functionality of a simplex.
Simplex(int[]) - Constructor for class edu.stanford.math.plex4.homology.chain_basis.Simplex: This constructor initializes the simplex from a supplied array of integers.
simplex_index - Variable in class edu.stanford.math.plex.SimplexStream.Stack
simplex_index - Variable in class edu.stanford.math.plex.SimplexStream.Stack.StackIterator
simplex_reverse_sort(int[]) - Static method in class edu.stanford.math.plex.Simplex: Sort a set of vertices into decreasing order, as needed for some Simplex operations.
simplex_table - Variable in class edu.stanford.math.plex.ExplicitStream
SimplexComparator - Class in edu.stanford.math.plex4.homology.chain_basis: This class defines the standard ordering on the Simplex class and implements the Comparator interface.
SimplexFaceIterator - Class in edu.stanford.math.plex: The SimplexFaceIterator class.
SimplexFaceIterator() - Constructor for class edu.stanford.math.plex.SimplexFaceIterator
SimplexFaceIterator(int[], int) - Constructor for class edu.stanford.math.plex.SimplexFaceIterator: Construct a new iterator for faces of a simplex given by an array.
SimplexFaceIterator(Simplex, int) - Constructor for class edu.stanford.math.plex.SimplexFaceIterator: Construct a new iterator for the faces specified dimension.
simplexIndex(Simplex) - Method in class edu.stanford.math.plex.SimplexStream.Stack
SimplexPair - Class in edu.stanford.math.plex4.homology.chain_basis
SimplexPair(Simplex, Simplex) - Constructor for class edu.stanford.math.plex4.homology.chain_basis.SimplexPair
SimplexPair(int[], int[]) - Constructor for class edu.stanford.math.plex4.homology.chain_basis.SimplexPair
SimplexPair(ObjectObjectPair<Simplex, Simplex>) - Constructor for class edu.stanford.math.plex4.homology.chain_basis.SimplexPair
SimplexPairComparator - Class in edu.stanford.math.plex4.homology.chain_basis
SimplexStack(int, int) - Static method in class edu.stanford.math.plex.Plex: Create an empty SimplexStream.Stack.
SimplexStream - Class in edu.stanford.math.plex: An instance of the abstract class SimplexStream provides the simplices of a filtered complex in lexicographic order on persistence index and dimension.
SimplexStream() - Constructor for class edu.stanford.math.plex.SimplexStream
SimplexStream.ComparisonType - Enum in edu.stanford.math.plex
SimplexStream.Head - Class in edu.stanford.math.plex: A Head provides the FO part of a FIFO queue when attached to a Tail to which simplices have been enqueued.
SimplexStream.Head() - Constructor for class edu.stanford.math.plex.SimplexStream.Head
SimplexStream.Head(SimplexStream.Tail) - Constructor for class edu.stanford.math.plex.SimplexStream.Head
SimplexStream.Stack - Class in edu.stanford.math.plex: Stack is a multiway segmented stack for sorted storage of simplices.
SimplexStream.Stack() - Constructor for class edu.stanford.math.plex.SimplexStream.Stack
SimplexStream.Stack(int, int) - Constructor for class edu.stanford.math.plex.SimplexStream.Stack: Constructor for Stack.
SimplexStream.Stack.Segment - Class in edu.stanford.math.plex
SimplexStream.Stack.Segment() - Constructor for class edu.stanford.math.plex.SimplexStream.Stack.Segment
SimplexStream.Stack.Segment(int) - Constructor for class edu.stanford.math.plex.SimplexStream.Stack.Segment
SimplexStream.Stack.StackIterator - Class in edu.stanford.math.plex: Instances provide Iterator for non-destructive iterating over Stack entries.
SimplexStream.Stack.StackIterator() - Constructor for class edu.stanford.math.plex.SimplexStream.Stack.StackIterator
SimplexStream.Stack.StackIterator(SimplexStream.Stack) - Constructor for class edu.stanford.math.plex.SimplexStream.Stack.StackIterator
SimplexStream.Stack.StackIterator(SimplexStream.Stack, int) - Constructor for class edu.stanford.math.plex.SimplexStream.Stack.StackIterator
SimplexStream.Tail - Class in edu.stanford.math.plex: An instance of Tail provides the FI part of a FIFO queue.
SimplexStream.Tail() - Constructor for class edu.stanford.math.plex.SimplexStream.Tail
SimplexStream.Tail(int) - Constructor for class edu.stanford.math.plex.SimplexStream.Tail
SimplexStreamExamples - Class in edu.stanford.math.plex4.examples: This class contains various functions for producing examples of filtered and static simplicial complexes.
SimplexStreamExamples() - Constructor for class edu.stanford.math.plex4.examples.SimplexStreamExamples
SimplexStreamReaderWriter - Class in edu.stanford.math.plex4.io
SimplexStreamUtility - Class in edu.stanford.math.plex4.homology.zigzag.bootstrap
SimplexStreamUtility() - Constructor for class edu.stanford.math.plex4.homology.zigzag.bootstrap.SimplexStreamUtility
SimplexTable(int) - Static method in class edu.stanford.math.plex.Plex: Make a new SimplexTable.
SimplexTable - Class in edu.stanford.math.plex: A SimplexTable is an interning table for instances of Simplex.
SimplexTable() - Constructor for class edu.stanford.math.plex.SimplexTable
SimplexTable(int) - Constructor for class edu.stanford.math.plex.SimplexTable: Make a new SimplexTable.
SimplexTable.SimpleTableIterator - Class in edu.stanford.math.plex: Instances provide Iterator for non-destructive iterating over entries.
SimplexTable.SimpleTableIterator(SimplexTable) - Constructor for class edu.stanford.math.plex.SimplexTable.SimpleTableIterator
simplices - Variable in class edu.stanford.math.plex.ExplicitStream
SimplicialComplexOperations - Class in edu.stanford.math.plex4.examples: This class contains various functions for creating new simplicial complexes out of old ones.
SimplicialComplexOperations() - Constructor for class edu.stanford.math.plex4.examples.SimplicialComplexOperations
SingleLinkageClustering - Class in edu.stanford.math.clustering
SingleLinkageClustering(AbstractIntMetricSpace) - Constructor for class edu.stanford.math.clustering.SingleLinkageClustering
size() - Method in class edu.stanford.math.clustering.DisjointSetSystem
size() - Method in class edu.stanford.math.plex.Cone
size() - Method in class edu.stanford.math.plex.ExplicitStream: How many simplices are in the stream?
size() - Method in class edu.stanford.math.plex.LazyWitnessStream: How many simplices are in the stream?
size() - Method in class edu.stanford.math.plex.PointData.Discrete.DSS
size() - Method in class edu.stanford.math.plex.RipsStream: How many simplices are in the stream?
size() - Method in class edu.stanford.math.plex.SimplexStream: How many simplices are in the stream?
size - Variable in class edu.stanford.math.plex.SimplexStream.Stack
size() - Method in class edu.stanford.math.plex.SimplexStream.Stack: How many simplices are in the stream?
size - Variable in class edu.stanford.math.plex.SimplexTable
size() - Method in class edu.stanford.math.plex.SimplexTable: The number of simplices that have been interned.
size() - Method in class edu.stanford.math.plex.TmpStream
size() - Method in class edu.stanford.math.plex.WitnessStream: How many simplices are in the stream?
size() - Method in class edu.stanford.math.plex4.kd.KDEuclideanMetricSpace
size() - Method in class edu.stanford.math.plex4.metric.impl.ExplicitMetricSpace
size() - Method in class edu.stanford.math.plex4.metric.impl.ObjectSearchableFiniteMetricSpace
size() - Method in interface edu.stanford.math.plex4.metric.interfaces.AbstractIntMetricSpace: This function returns the number of points in the metric space.
size() - Method in class edu.stanford.math.plex4.metric.landmark.LandmarkSelector
size() - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
size() - Method in class edu.stanford.math.plex4.streams.utility.SkeletalMetric
SkeletalMetric - Class in edu.stanford.math.plex4.streams.utility: This class implements a metric on a simplicial complex.
SkeletalMetric(AbstractFilteredStream<Simplex>) - Constructor for class edu.stanford.math.plex4.streams.utility.SkeletalMetric
skip_to_next_index_pair() - Method in class edu.stanford.math.plex.ExplicitStream.ExplicitStreamIterator
skip_to_next_index_pair() - Method in class edu.stanford.math.plex.ExplicitStream
solve() - Method in class edu.stanford.math.plex4.bottleneck.FordFulkerson
sort(int[], int, int, int[], boolean) - Static method in class edu.stanford.math.plex.PlexSort: Take an array of indices and sort them by the values in an array.
sort(int[], int, int, double[], boolean) - Static method in class edu.stanford.math.plex.PlexSort
sort(int[], int[], boolean) - Static method in class edu.stanford.math.plex.PlexSort
sort(int[], int[]) - Static method in class edu.stanford.math.plex.PlexSort
sort(int[], double[], boolean) - Static method in class edu.stanford.math.plex.PlexSort
sort(int[], double[]) - Static method in class edu.stanford.math.plex.PlexSort
sorted_intersection_count(int[], int[]) - Static method in class edu.stanford.math.plex.Plex: Compute the overlap size for two sorted arrays using the zipper algorithm.
SortedStorageStructure<T> - Class in edu.stanford.math.plex4.streams.storage_structures: This class implements an in-memory stream storage mechanism where all of the elements are held in an in-memory collection in fully sorted order.
SortedStorageStructure(Comparator<T>) - Constructor for class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure: This construction initializes the class with a comparator for comparing the basis elements.
SphereGraph - Class in edu.stanford.math.plex4.graph.random
SphereGraph(int, int) - Constructor for class edu.stanford.math.plex4.graph.random.SphereGraph
ss - Variable in class edu.stanford.math.plex.PointData.Discrete.DSS
ssiterator - Variable in class edu.stanford.math.plex.Cone
sstream - Variable in class edu.stanford.math.plex.Cone
st - Variable in class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
stack - Variable in class edu.stanford.math.plex.LazyWitnessStream
stack - Variable in class edu.stanford.math.plex.RipsStream
stack - Variable in class edu.stanford.math.plex.WitnessStream
STACK_SEGMENT_LENGTH - Static variable in class edu.stanford.math.plex.SimplexStream.Stack
start() - Method in class edu.stanford.math.plex.MappedBufferData: The first data dimension of the space.
start - Variable in class edu.stanford.math.plex.PersistenceBasisInterval.Float
start - Variable in class edu.stanford.math.plex.PersistenceBasisInterval.Int
start - Variable in class edu.stanford.math.plex.PersistenceInterval.Float
start - Variable in class edu.stanford.math.plex.PersistenceInterval.Int
start - Variable in class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
start_size - Variable in class edu.stanford.math.plex.SimplexTable.SimpleTableIterator
startInterval(K, I, int, G) - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
startNewCell(String) - Method in class edu.stanford.math.plex4.io.MatlabWriter: This function begins a new cell in the Matlab file.
State - Enum in <Unnamed>
StaticConverter - Class in edu.stanford.math.plex4.homology.filtration: This class implements the FiltrationConverter interface for static complexes.
StochasticBlockmodel - Class in edu.stanford.math.plex4.graph.random
StochasticBlockmodel(int, double[][]) - Constructor for class edu.stanford.math.plex4.graph.random.StochasticBlockmodel
stop() - Method in class edu.stanford.math.plex.MappedBufferData: The last data dimension of the space.
storageStructure - Variable in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream: This object implements the actual storage structure for the stream.
stpath() - Method in class edu.stanford.math.plex4.bottleneck.FordFulkerson
stream1 - Variable in class edu.stanford.math.plex4.streams.derived.TensorStream: The first factor in the tensor product.
stream2 - Variable in class edu.stanford.math.plex4.streams.derived.TensorStream: The second factor in the tensor product.
StreamStorageStructure<T> - Interface in edu.stanford.math.plex4.streams.storage_structures: This interface defines the functionality of a stream storage structure.
StreamStorageStructureFactory - Class in edu.stanford.math.plex4.streams.storage_structures: This class contains various convenience functions for constructing stream storage structures.
StreamStorageStructureFactory() - Constructor for class edu.stanford.math.plex4.streams.storage_structures.StreamStorageStructureFactory
StreamUtility - Class in edu.stanford.math.plex4.streams.utility: This class contains various static functions for querying and manipulating filtered chain complexes.
StreamUtility() - Constructor for class edu.stanford.math.plex4.streams.utility.StreamUtility
string - Variable in class edu.stanford.math.mapper.HistogramCreator
style - Variable in class edu.stanford.math.plex.PlexMessageWindow
subset(Simplex) - Method in class edu.stanford.math.plex.Simplex: Is this a subset of s?
subset(Simplex, int[], int[]) - Method in class edu.stanford.math.plex.Simplex: Is this a subset of s?
support - Variable in class edu.stanford.math.plex.Cone

T

table - Variable in class edu.stanford.math.plex.SimplexTable
Table - Class in edu.stanford.math.plex4.io: This class holds a table of string values.
Table() - Constructor for class edu.stanford.math.plex4.io.Table
TensorStream<T,U> - Class in edu.stanford.math.plex4.streams.derived: This implements the tensor product of two filtered chain complexes.
TensorStream(AbstractFilteredStream<T>, AbstractFilteredStream) - Constructor for class edu.stanford.math.plex4.streams.derived.TensorStream: This constructor initializes the stream from two underlying filtered chain complexes.
textPane - Variable in class edu.stanford.math.plex.PlexMessageWindow
thereIsaBackgroundImage - Variable in class edu.stanford.math.plex.BCPlot
thresholdByDistance(double) - Method in class edu.stanford.math.clustering.HierarchicalClustering
thresholdByNumClusters(int) - Method in class edu.stanford.math.clustering.HierarchicalClustering
tickGap - Variable in class edu.stanford.math.plex.BCPlot
tickMajorPlacement - Variable in class edu.stanford.math.plex.BCPlot
tickUpperBoundColor - Variable in class edu.stanford.math.plex.BCPlot
title - Variable in class edu.stanford.math.plex4.io.Table
TmpStream - Class in edu.stanford.math.plex: The TmpStream class.
TmpStream(Simplex[]) - Constructor for class edu.stanford.math.plex.TmpStream
toColumnVector(DoubleMatrix1D, String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toColumnVector(DoubleMatrix1D) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toColumnVector(int[], String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toColumnVector(int[]) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toColumnVector(double[], String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toColumnVector(double[]) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toColumnVector(Iterable<T>, String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toColumnVector(Iterable<T>) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toCSVString(String, boolean, boolean) - Method in class edu.stanford.math.plex4.io.Table: This function creates a string holding the contents of the table in comma separated format.
toDouble(int[]) - Static method in class edu.stanford.math.plex.ExplicitStream
toDouble(int[][]) - Static method in class edu.stanford.math.plex.ExplicitStream
toDouble() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Float: Represent a PersistenceBasisInterval.Int as a double[].
toDouble() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Int: Represent a PersistenceBasisInterval.Int as a double[].
toDouble() - Method in class edu.stanford.math.plex.PersistenceBasisInterval: Return the start/endpoints as double[].
toDouble() - Method in class edu.stanford.math.plex.PersistenceInterval.Float: Represent a PersistenceInterval.Int as a double[].
toDouble() - Method in class edu.stanford.math.plex.PersistenceInterval.Int: Represent a PersistenceInterval.Int as a double[].
toDouble() - Method in class edu.stanford.math.plex.PersistenceInterval: Return the start/endpoints as double[].
toDoubleFormalSum(ObjectSparseFormalSum<R, M>) - Static method in class edu.stanford.math.plex4.streams.derived.HomStream: This function converts an ObjectSparseFormalSum to a DoubleSparseFormalSum object.
toDoubleFormalSum(List<ObjectSparseFormalSum<R, M>>) - Static method in class edu.stanford.math.plex4.streams.derived.HomStream: This function converts a list of ObjectSparseFormalSum objects to DoubleSparseFormalSum objects.
toGeometricSimplexStream(AbstractUndirectedGraph, double[][]) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility
toInt(double[]) - Static method in class edu.stanford.math.plex.ExplicitStream
toInt(double[][]) - Static method in class edu.stanford.math.plex.ExplicitStream
toMatrix(DoubleMatrix2D, String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toMatrix(double[][], String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toMatrix(int[][], String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toMatrix(DoubleMatrix2D) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toMatrix(double[][]) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toMatrix(int[][]) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toPersistenceInterval() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Float
toPersistenceInterval() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Int
toPersistenceInterval() - Method in class edu.stanford.math.plex.PersistenceBasisInterval: Conversion to PersistenceInterval
toPrettyString(String) - Method in class edu.stanford.math.plex4.io.Table: This function returns a string holding the contents of the table.
toRowVector(DoubleMatrix1D, String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toRowVector(DoubleMatrix1D) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toRowVector(int[], String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toRowVector(int[]) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toRowVector(double[], String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toRowVector(double[]) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toRowVector(Iterable<T>, String) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toRowVector(Iterable<T>) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
Torus(int, int) - Static method in class edu.stanford.math.plex.Plex: Create a Torus with a given granulatity.
Torus() - Static method in class edu.stanford.math.plex.TmpStream
Torus - Class in edu.stanford.math.plex: A Torus instance is discrete simulation of a d-dimensional torus.
Torus(double[], int) - Constructor for class edu.stanford.math.plex.Torus: Make a Torus with a given data array.
Torus(int, int) - Constructor for class edu.stanford.math.plex.Torus: Make an n-way grid on the unit Torus.
Torus() - Constructor for class edu.stanford.math.plex.Torus
TorusGraph - Class in edu.stanford.math.plex4.graph.random
TorusGraph(int, int, int) - Constructor for class edu.stanford.math.plex4.graph.random.TorusGraph
TorusGraph(int, int) - Constructor for class edu.stanford.math.plex4.graph.random.TorusGraph
toSimplexStream(AbstractUndirectedGraph) - Static method in class edu.stanford.math.plex4.graph.utility.GraphUtility
toString() - Method in class edu.stanford.math.mapper.HistogramCreator
toString() - Method in class edu.stanford.math.plex.Chain: Represent a Chain as a String.
toString() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Float: Represent a PersistenceBasisInterval.Float as a String.
toString() - Method in class edu.stanford.math.plex.PersistenceBasisInterval.Int: Represent a PersistenceBasisInterval.Int as a String.
toString() - Method in class edu.stanford.math.plex.PersistenceBasisInterval: Represent a PersistenceBasisInterval as a String.
toString() - Method in class edu.stanford.math.plex.PersistenceInterval.Float: Represent a PersistenceInterval.Float as a String.
toString() - Method in class edu.stanford.math.plex.PersistenceInterval.Int: Represent a PersistenceInterval.Int as a String.
toString() - Method in class edu.stanford.math.plex.PersistenceInterval: Represent a PersistenceInterval as a String.
toString() - Method in class edu.stanford.math.plex.Plex.BettiNumbers: Make BettiNumbers printable.
toString(int[], int) - Static method in class edu.stanford.math.plex.Plex: Take an array of int and make a string.
toString(int[]) - Static method in class edu.stanford.math.plex.Plex: Take an array of int and make a string.
toString(byte[], int) - Static method in class edu.stanford.math.plex.Plex: Take an array of byte and make a string.
toString(byte[]) - Static method in class edu.stanford.math.plex.Plex: Take an array of byte and make a string.
toString(int[][], int) - Static method in class edu.stanford.math.plex.Plex: Take an array of int[] and make a string.
toString(int[][]) - Static method in class edu.stanford.math.plex.Plex: Take an int[][] and make a string.
toString(double[], int) - Static method in class edu.stanford.math.plex.Plex: Take an array of double and make a string.
toString(double[]) - Static method in class edu.stanford.math.plex.Plex: Take an array of double and make a string.
toString(double[][], int) - Static method in class edu.stanford.math.plex.Plex: Take an array of double[] and make a string.
toString(double[][]) - Static method in class edu.stanford.math.plex.Plex: Take an double[][] and make a string.
toString(long[], int) - Static method in class edu.stanford.math.plex.Plex: Take an array of long and make a string.
toString(long[]) - Static method in class edu.stanford.math.plex.Plex: Take an array of long and make a string.
toString() - Method in class edu.stanford.math.plex.Simplex: Represent a Simplex as a String.
toString() - Method in class edu.stanford.math.plex.SimplexStream.Head
toString() - Method in class edu.stanford.math.plex.SimplexStream.Stack.Segment
toString() - Method in class edu.stanford.math.plex.SimplexStream.Stack
toString() - Method in class edu.stanford.math.plex.SimplexStream.Tail
toString() - Method in class edu.stanford.math.plex4.bottleneck.FlowEdge
toString() - Method in class edu.stanford.math.plex4.bottleneck.FordFulkersonEdge
toString() - Method in class edu.stanford.math.plex4.bottleneck.FordFulkersonNode
toString() - Method in class edu.stanford.math.plex4.graph.random.BAGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.BinaryHierarchicalGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.BinaryTreeGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.CircleGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.ClusteredERGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.ErdosRenyiGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.ForestFireGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.HierarchicalERGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.KNearestNeighborsGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.PrescribedDegrees
toString() - Method in class edu.stanford.math.plex4.graph.random.RandomGeometricGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.SphereGraph
toString() - Method in class edu.stanford.math.plex4.graph.random.StochasticBlockmodel
toString() - Method in class edu.stanford.math.plex4.graph.random.TorusGraph
toString() - Method in class edu.stanford.math.plex4.homology.barcodes.Interval
toString() - Method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor
toString() - Method in class edu.stanford.math.plex4.homology.chain_basis.Cell
toString() - Method in class edu.stanford.math.plex4.homology.chain_basis.Simplex
toString() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalDescriptor
toString() - Method in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
toString() - Method in class edu.stanford.math.plex4.io.Table: This function returns the string representation of the table.
toString() - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
toStringList(List<String>) - Static method in class edu.stanford.math.plex4.io.MatlabWriter
toUnweightedGraph() - Method in class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.homology.filtration.FiltrationConverter
transform(PersistenceInvariantDescriptor<X, G>, ObjectObjectFunction<X, Y>) - Static method in class edu.stanford.math.plex4.homology.filtration.FiltrationUtility
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.interop.Plex3Stream
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.streams.derived.DualStream
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.streams.derived.TensorStream
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.streams.derived.TruncatedStream
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.streams.impl.ExplicitStream
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.streams.impl.FlagComplexStream: This function transforms the given collection of filtration index barcodes into filtration value barcodes.
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.streams.impl.GeometricSimplexStream
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.streams.impl.WitnessStream: This function transforms the given collection of filtration index barcodes into filtration value barcodes.
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in interface edu.stanford.math.plex4.streams.interfaces.AbstractFilteredStream: This function transforms the given collection of filtration index barcodes into filtration value barcodes.
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in interface edu.stanford.math.plex4.streams.multi.AbstractMultifilteredStream: This function transforms the given collection of filtration index barcodes into filtration value barcodes.
transform(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Method in class edu.stanford.math.plex4.streams.multi.PrimitiveMultifilteredStream
transformByIdentity(PersistenceInvariantDescriptor<Interval<Integer>, G>) - Static method in class edu.stanford.math.plex4.homology.filtration.FiltrationUtility
translateAndScale(double, double, double, float) - Static method in class edu.stanford.math.plex4.visualization.PointCloudScaling
truncate(List<Interval<Double>>, double, double) - Static method in class edu.stanford.math.plex4.bottleneck.BottleneckDistance
TruncatedPriorityQueue<T> - Class in edu.stanford.math.plex4.metric.impl: This class is used for holding the set of k-indices with the lowest ranks or values.
TruncatedPriorityQueue(int) - Constructor for class edu.stanford.math.plex4.metric.impl.TruncatedPriorityQueue
TruncatedStream<T> - Class in edu.stanford.math.plex4.streams.derived
TruncatedStream(AbstractFilteredStream<T>, double) - Constructor for class edu.stanford.math.plex4.streams.derived.TruncatedStream
turnOffCommentMode() - Method in class edu.stanford.math.plex4.io.MatlabWriter: This function turns off the comment mode.
turnOnCommentMode() - Method in class edu.stanford.math.plex4.io.MatlabWriter: This function turns on the comment mode, meaning that any output will be written as a comment and not Matlab code.

U

UndirectedListEdgeIterator - Class in edu.stanford.math.plex4.graph
UndirectedListEdgeIterator(TIntObjectHashMap<TIntHashSet>) - Constructor for class edu.stanford.math.plex4.graph.UndirectedListEdgeIterator
UndirectedListGraph - Class in edu.stanford.math.plex4.graph: This class implements the functionality of an undirected graph.
UndirectedListGraph(int) - Constructor for class edu.stanford.math.plex4.graph.UndirectedListGraph: Constructor which initializes the graph to consist of disconnected vertices.
UndirectedListGraph(int, TIntObjectHashMap<TIntHashSet>) - Constructor for class edu.stanford.math.plex4.graph.UndirectedListGraph
UndirectedListGraph(AbstractUndirectedGraph) - Constructor for class edu.stanford.math.plex4.graph.UndirectedListGraph: This constructor initializes the graph with the contents of another graph.
UndirectedListGraph(int[][]) - Constructor for class edu.stanford.math.plex4.graph.UndirectedListGraph: Constructor which initializes the graph to contain the edges given in the specified adjacency matrix.
UndirectedWeightedListGraph - Class in edu.stanford.math.plex4.graph: This class implements the functionality of an undirected weighted graph.
UndirectedWeightedListGraph(int) - Constructor for class edu.stanford.math.plex4.graph.UndirectedWeightedListGraph: Constructor which initializes the graph to consist of disconnected vertices.
uniformArray(int) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function returns an array of uniformly distributed random numbers.
uniformGenerator - Variable in class edu.stanford.math.plex4.graph.random.ForestFireGraph
uniformMatrix(int, int) - Static method in class edu.stanford.math.plex4.utility.RandomUtility: This function returns a matrix containing uniformly distributed random numbers.
union(int, int) - Method in class edu.stanford.math.clustering.DisjointSetSystem
union(PersistenceInvariantDescriptor<I, G>, PersistenceInvariantDescriptor<I, G>) - Static method in class edu.stanford.math.plex4.homology.barcodes.PersistenceInvariantDescriptor: This function computes the union of two collections of persistence invariants.
union(int, int) - Method in class edu.stanford.math.plex4.homology.nonautogen.DisjointSetSystem: Deprecated.
union(int[], int[]) - Static method in class edu.stanford.math.plex4.utility.ArrayUtility
unitsPerPixel - Variable in class edu.stanford.math.plex.BCPlot
update32(byte, int, int[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 32-bit CRC calculation for a single byte.
update32(short, int, int[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 32-bit CRC calculation for a single short.
update32(int, int, int[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 32-bit CRC calculation for a single int.
update32(long, int, int[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 32-bit CRC calculation for a single long.
update32l(long, int, int[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 32-bit CRC calculation for a single byte.
update64(byte, long, long[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 64-bit CRC calculation for a single byte.
update64(short, long, long[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 64-bit CRC calculation for a single short.
update64(int, long, long[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 64-bit CRC calculation for a single int.
update64(long, long, long[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 64-bit CRC calculation for a single long.
update64l(long, long, long[]) - Static method in class edu.stanford.math.plex.CRC: Incremental 64-bit CRC calculation for a single byte.
update_hash(int, long) - Static method in class edu.stanford.math.plex.CRC: Incremental 64-bit CRC for an integer.
update_hash(long, long) - Static method in class edu.stanford.math.plex.CRC: Incremental 64-bit CRC for a long.
updateOrAddElement(T, int) - Method in class edu.stanford.math.plex4.streams.storage_structures.SortedStorageStructure
updateWitnessInformation(int, double, int...) - Method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
updateWitnessInformationInternalIndices(int, double, int...) - Method in class edu.stanford.math.plex4.streams.impl.LazyWitnessStream
upperBoundFontColor - Variable in class edu.stanford.math.plex.BCPlot
upperEntries(int[], int) - Static method in class edu.stanford.math.plex4.homology.utility.HomologyUtility: This function returns the last entries of the supplied array starting from the index k.
upperMargin - Variable in class edu.stanford.math.plex.BCPlot
usage() - Static method in class bsh.commands.log
usage() - Static method in class bsh.commands.setLogging
use(int) - Method in class edu.stanford.math.plex.PointData.Predicate: Is the point i interesting to this predicate?
useLeftClosedDefault - Variable in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection
useLeftClosedIntervals - Variable in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker
useMessageWindow - Static variable in class edu.stanford.math.plex.Plex
useMessageWindow(boolean) - Static method in class edu.stanford.math.plex.Plex: Use a PlexMessageWindow for messages?
useMessageWindow() - Static method in class edu.stanford.math.plex.Plex: Should we use a PlexMessageWindow for messages?
useRightClosedDefault - Variable in class edu.stanford.math.plex4.homology.barcodes.AnnotatedBarcodeCollection
useRightClosedIntervals - Variable in class edu.stanford.math.plex4.homology.zigzag.IntervalTracker

V

v1() - Method in class edu.stanford.math.plex.Packed2Simplex
v1() - Method in class edu.stanford.math.plex.Packed4Simplex
v1() - Method in class edu.stanford.math.plex.Packed6Simplex
v1() - Method in class edu.stanford.math.plex.Packed8Simplex
v2() - Method in class edu.stanford.math.plex.Packed2Simplex
v2() - Method in class edu.stanford.math.plex.Packed4Simplex
v2() - Method in class edu.stanford.math.plex.Packed6Simplex
v2() - Method in class edu.stanford.math.plex.Packed8Simplex
v3() - Method in class edu.stanford.math.plex.Packed4Simplex
v3() - Method in class edu.stanford.math.plex.Packed6Simplex
v3() - Method in class edu.stanford.math.plex.Packed8Simplex
v4() - Method in class edu.stanford.math.plex.Packed4Simplex
v4() - Method in class edu.stanford.math.plex.Packed6Simplex
v4() - Method in class edu.stanford.math.plex.Packed8Simplex
v5() - Method in class edu.stanford.math.plex.Packed6Simplex
v5() - Method in class edu.stanford.math.plex.Packed8Simplex
v6() - Method in class edu.stanford.math.plex.Packed6Simplex
v6() - Method in class edu.stanford.math.plex.Packed8Simplex
v7() - Method in class edu.stanford.math.plex.Packed8Simplex
v8() - Method in class edu.stanford.math.plex.Packed8Simplex
validate(double[][], double) - Method in class edu.stanford.math.plex.BCPlot: Validate the upperBound and the values used for the Barcode Plot
validate() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream: This function validates the stream to make sure that it contains a valid filtered simplicial or cell complex.
validateVerbose() - Method in class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream: This function validates the stream to make sure that it contains a valid filtered simplicial or cell complex.
valueOf(String) - Static method in enum edu.stanford.math.plex.PersistenceBasis.SimplexType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.stanford.math.plex.SimplexStream.ComparisonType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum edu.stanford.math.plex4.graph.random.GraphInstanceGenerator.ImplementationType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum State: Returns the enum constant of this type with the specified name.
values - Variable in class edu.stanford.math.mapper.HistogramCreator
values() - Static method in enum edu.stanford.math.plex.PersistenceBasis.SimplexType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.stanford.math.plex.SimplexStream.ComparisonType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum edu.stanford.math.plex4.graph.random.GraphInstanceGenerator.ImplementationType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum State: Returns an array containing the constants of this enum type, in the order they are declared.
vec - Variable in class edu.stanford.math.plex.SimplexTable.SimpleTableIterator
verify() - Method in class edu.stanford.math.plex.ExplicitStream: Quietly verify the ExplicitStream.
verify(boolean) - Method in class edu.stanford.math.plex.ExplicitStream: Verify the ExplicitStream.
verify() - Method in class edu.stanford.math.plex.SimplexStream: Check the stream as much as possible.
verifyAllNonNull(Collection<T>) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyClosedInterval(int, int, int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyClosedInterval(double, double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyDimension() - Method in class edu.stanford.math.plex4.homology.chain_basis.Cell: This function checks to see if the cell has been glued to boundary elements all of the same dimension.
verifyEqual(int, int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyEqual(double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyFalse(boolean) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyFalse(boolean, String) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyGreaterThan(int, int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyGreaterThan(double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyGreaterThanOrEqual(int, int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyGreaterThanOrEqual(double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyIndex(int, int, int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility: This function checks to see if index is in the set {lowerBound, ..., upperBound - 1}.
verifyIndex(int, int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility: This function checks to see if index is in the set {0, ..., upperBound - 1}.
verifyLeftHalfOpenInterval(double, double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyLessThan(int, int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyLessThan(double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyLessThanOrEqual(int, int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyLessThanOrEqual(double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNegative(int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNegative(double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonEmpty(Collection<T>) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonEmpty(int[]) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonEmpty(double[]) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonEqual(int, int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonEqual(double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonNegative(int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonNegative(double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonNull(Object) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonPositive(int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonPositive(double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonZero(int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyNonZero(double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyOpenInterval(double, double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyPositive(int) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyPositive(double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyRightHalfOpenInterval(double, double, double) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyTrue(boolean) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
verifyTrue(boolean, String) - Static method in class edu.stanford.math.plex4.utility.ExceptionUtility
VERTEX_BIT_SZ - Static variable in class edu.stanford.math.plex.Packed2Simplex
VERTEX_BIT_SZ - Static variable in class edu.stanford.math.plex.Packed4Simplex
VERTEX_BIT_SZ - Static variable in class edu.stanford.math.plex.Packed6Simplex
VERTEX_BIT_SZ - Static variable in class edu.stanford.math.plex.Packed8Simplex
vertex_sort(int[]) - Static method in class edu.stanford.math.plex.Simplex: Sort a set of vertices into increasing order, as needed for some Simplex operations.
vertices() - Method in class edu.stanford.math.plex.Packed2Simplex: Returns the indices of self as an array.
vertices(int[]) - Method in class edu.stanford.math.plex.Packed2Simplex: Returns the indices of self in the given array argument.
vertices() - Method in class edu.stanford.math.plex.Packed4Simplex: Returns the indices of self as an array.
vertices(int[]) - Method in class edu.stanford.math.plex.Packed4Simplex: Returns the indices of self in the given array argument.
vertices() - Method in class edu.stanford.math.plex.Packed6Simplex: Returns the indices of self as an array.
vertices(int[]) - Method in class edu.stanford.math.plex.Packed6Simplex: Returns the indices of self in the given array argument.
vertices() - Method in class edu.stanford.math.plex.Packed8Simplex: Returns the indices of self as an array.
vertices(int[]) - Method in class edu.stanford.math.plex.Packed8Simplex: Returns the indices of self in the given array argument.
vertices() - Method in class edu.stanford.math.plex.Simplex: Returns the indices of self as an array.
vertices(int[]) - Method in class edu.stanford.math.plex.Simplex: Returns the indices of self as an array.
vertices - Variable in class edu.stanford.math.plex.SimplexFaceIterator
VietorisRipsBootstrapper - Class in edu.stanford.math.plex4.homology.zigzag.bootstrap
VietorisRipsBootstrapper(double[][], double, int, List<int[]>) - Constructor for class edu.stanford.math.plex4.homology.zigzag.bootstrap.VietorisRipsBootstrapper
VietorisRipsBootstrapper(double[][], double, int, int, int) - Constructor for class edu.stanford.math.plex4.homology.zigzag.bootstrap.VietorisRipsBootstrapper
VietorisRipsStream<T> - Class in edu.stanford.math.plex4.streams.impl: This class implements the Vietoris-Rips filtered simplicial complex.
VietorisRipsStream(AbstractSearchableMetricSpace<T>, double, int) - Constructor for class edu.stanford.math.plex4.streams.impl.VietorisRipsStream: Constructor which initializes the complex with a metric space.
VietorisRipsStream(AbstractSearchableMetricSpace<T>, double, int, int) - Constructor for class edu.stanford.math.plex4.streams.impl.VietorisRipsStream
VietorisRipsStream(AbstractSearchableMetricSpace<T>, double, int, int, StreamStorageStructure<Simplex>) - Constructor for class edu.stanford.math.plex4.streams.impl.VietorisRipsStream
VietorisRipsStream(AbstractSearchableMetricSpace<T>, double, int, int[]) - Constructor for class edu.stanford.math.plex4.streams.impl.VietorisRipsStream
VietorisRipsStream(AbstractSearchableMetricSpace<T>, double[], int) - Constructor for class edu.stanford.math.plex4.streams.impl.VietorisRipsStream

W

WeightedBipartiteGraph - Class in edu.stanford.math.plex4.bottleneck
WeightedBipartiteGraph(int) - Constructor for class edu.stanford.math.plex4.bottleneck.WeightedBipartiteGraph
whichSegmentHasX(double[], double) - Method in class edu.stanford.math.plex4.graph.random.BAGraph: Returns the segment i such that x is in [p[i],p[i+1]].
whichSegmentHasX(double[], double) - Method in class edu.stanford.math.plex4.graph.random.PrescribedDegrees: Returns the segment i such that x is in [p[i],p[i+1]].
widthOfSideRegionUsedForPlotLegendRulerLabels - Variable in class edu.stanford.math.plex.BCPlot
WitnessBicomplex<T> - Class in edu.stanford.math.plex4.streams.impl
WitnessBicomplex(WitnessStream<T>, WitnessStream<T>, int) - Constructor for class edu.stanford.math.plex4.streams.impl.WitnessBicomplex
WitnessBootstrapper<T> - Class in edu.stanford.math.plex4.homology.zigzag.bootstrap
WitnessBootstrapper(AbstractSearchableMetricSpace<T>, List<LandmarkSelector<T>>, int, double) - Constructor for class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
WitnessBootstrapper(AbstractSearchableMetricSpace<T>, double, int, int, int) - Constructor for class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
WitnessStream(double, int, double, int[], PointData) - Static method in class edu.stanford.math.plex.Plex: Make a stream of the simplices in a Witness complex for data.
WitnessStream - Class in edu.stanford.math.plex: A WitnessStream is an iterable Witness complex.
WitnessStream() - Constructor for class edu.stanford.math.plex.WitnessStream
WitnessStream<T> - Class in edu.stanford.math.plex4.streams.impl
WitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double, int) - Constructor for class edu.stanford.math.plex4.streams.impl.WitnessStream: Constructor which initializes the complex with a metric space.
WitnessStream(AbstractSearchableMetricSpace<T>, LandmarkSelector<T>, int, double, int[]) - Constructor for class edu.stanford.math.plex4.streams.impl.WitnessStream
write(String) - Method in class edu.stanford.math.plex4.io.MatlabWriter: This function writes a string to the file.
writeClearAll() - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeColumnVector(DoubleMatrix1D, String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeColumnVector(DoubleMatrix1D) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeColumnVector(double[], String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeColumnVector(double[]) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeColumnVector(int[], String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeColumnVector(int[]) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeColumnVector(Iterable<T>) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeColumnVector(Iterable<T>, String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeLine(String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeMatrix(DoubleMatrix2D, String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeMatrix(DoubleMatrix2D) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeMatrix(double[][], String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeMatrix(double[][]) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeMatrix(int[][], String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeMatrix(int[][]) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeRow(Map<X, IntSparseFormalSum<Integer>>, IntSparseFormalSum<X>, int) - Static method in class edu.stanford.math.plex4.homology.zigzag.BasisTrackingUtility
writeRowVector(DoubleMatrix1D, String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeRowVector(DoubleMatrix1D) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeRowVector(double[], String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeRowVector(double[]) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeRowVector(int[], String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeRowVector(int[]) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeRowVector(Iterable<T>) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeRowVector(Iterable<T>, String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeSparseMatrix(double[][], String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeSparseVector(double[], String) - Method in class edu.stanford.math.plex4.io.MatlabWriter
writeTextFile(String, String, boolean) - Static method in class edu.stanford.math.plex4.io.FileIOUtility: This function saves a string to a text file.
writeToFile(AbstractUndirectedGraph, String) - Method in class edu.stanford.math.plex4.graph.io.GraphDotWriter
writeToFile(PersistenceInvariantDescriptor<Interval<Double>, G>, int, double, String, String) - Method in class edu.stanford.math.plex4.io.BarcodeWriter
writeToFile(BufferedImage, String) - Method in class edu.stanford.math.plex4.io.BufferedImageWriter
writeToFile(double[][], String) - Method in class edu.stanford.math.plex4.io.DoubleArrayReaderWriter
writeToFile(T, String) - Method in interface edu.stanford.math.plex4.io.ObjectWriter
writeToFile(AbstractFilteredStream<Simplex>, String) - Method in class edu.stanford.math.plex4.io.SimplexStreamReaderWriter

X

x - Variable in class edu.stanford.math.plex4.visualization.Point2D
xi(int, int) - Method in class edu.stanford.math.plex.PointData.NSpace

Y

y - Variable in class edu.stanford.math.plex4.visualization.Point2D

Z

Z - Variable in class edu.stanford.math.plex4.homology.zigzag.HomologyBasisTracker
Z_chainModule - Variable in class edu.stanford.math.plex4.homology.zigzag.bootstrap.WitnessBootstrapper
zero(int) - Static method in class edu.stanford.math.plex.Chain
ZigZagHomology - Class in edu.stanford.math.plex4.homology.zigzag
ZigZagHomology(IntAbstractField, Comparator, int, int) - Constructor for class edu.stanford.math.plex4.homology.zigzag.ZigZagHomology: This constructor initializes the object with a field and a comparator on the basis type.

_

_chain - Variable in class edu.stanford.math.plex.Simplex
_findex - Variable in class edu.stanford.math.plex.Simplex: The filtration index of the Simplex.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _