edu.stanford.math.plex4.interop

Class Plex3Stream

java.lang.Object

edu.stanford.math.plex4.interop.Plex3Stream

All Implemented Interfaces:

AbstractFilteredStream<Simplex>, java.lang.Iterable<Simplex>

public class Plex3Stream
extends java.lang.Object
implements AbstractFilteredStream<Simplex>

This class is a wrapper around a plex 3 SimplexStream that implements the AbstractFilteredStream interface of plex 4.

Author:

Andrew Tausz

Constructor Summary

Constructors

Constructor and Description
Plex3Stream(SimplexStream plex3Stream)
Plex3Stream(SimplexStream plex3Stream, int[] vertexMapping)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	containsElement(Simplex basisElement) This function returns whether an element is contained in the stream.
void	finalizeStream() This function prepares the stream for use by a consumer, such as the PersistentHomology class.
java.util.Comparator<Simplex>	getBasisComparator() This function returns a comparator on the underlying basis type.
Simplex[]	getBoundary(Simplex basisElement) This function returns the elements in the boundary of the supplied basisElement, without the coefficients.
int[]	getBoundaryCoefficients(Simplex basisElement) This function returns the coefficients of the boundary of the supplied basis element.
int	getDimension(Simplex basisElement) This function returns the dimension of a basis element within the chain complex.
int	getFiltrationIndex(Simplex basisElement) This function returns the filtration index of the requested basis element.
double	getFiltrationValue(Simplex basisElement)
int	getMaximumFiltrationIndex() This function gets the maximum filtration index in the complex.
int	getMinimumFiltrationIndex() This function gets the minimum filtration index in the complex.
int	getSize() This function returns the total number of elements in the stream.
boolean	isFinalized() This function checks whether the finalize() function has been called.
java.util.Iterator<Simplex>	iterator()
<G> PersistenceInvariantDescriptor<Interval<java.lang.Double>,G>	transform(PersistenceInvariantDescriptor<Interval<java.lang.Integer>,G> barcodeCollection) This function transforms the given collection of filtration index barcodes into filtration value barcodes.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Plex3Stream

public Plex3Stream(SimplexStream plex3Stream)

Plex3Stream

public Plex3Stream(SimplexStream plex3Stream,
           int[] vertexMapping)

Method Detail

finalizeStream

public void finalizeStream()

Description copied from interface: AbstractFilteredStream

This function prepares the stream for use by a consumer, such as the PersistentHomology class. After finalization, the stream cannot not be modified by adding or removing elements. In practice, the finalize procedure will probably do some sorting and construction of data structures necessary for iterating through the stream.

Specified by:

finalizeStream in interface AbstractFilteredStream<Simplex>

getBoundary

public Simplex[] getBoundary(Simplex basisElement)

Description copied from interface: AbstractFilteredStream

This function returns the elements in the boundary of the supplied basisElement, without the coefficients. We do not integrate the elements of the boundary array with their respective coefficients since this interface is designed to be independent of the algebraic environment.

Specified by:

getBoundary in interface AbstractFilteredStream<Simplex>

Parameters:

basisElement - the element to get the boundary of

Returns:

an array containing the boundary elements of the queried element

getBoundaryCoefficients

public int[] getBoundaryCoefficients(Simplex basisElement)

Description copied from interface: AbstractFilteredStream

This function returns the coefficients of the boundary of the supplied basis element. Note that in many cases, this will be the standard array consisting of alternating signs: [1, -1, 1, -1, ...]. However, this will not always be the case. Thus this must be left abstract. Also note that the coefficients will always be integers.

Specified by:

getBoundaryCoefficients in interface AbstractFilteredStream<Simplex>

Parameters:

basisElement - the element to get the boundary coefficients of

Returns:

an array containing the boundary coefficients of the queried element

getDimension

public int getDimension(Simplex basisElement)

Description copied from interface: AbstractFilteredStream

This function returns the dimension of a basis element within the chain complex.

Specified by:

getDimension in interface AbstractFilteredStream<Simplex>

Parameters:

basisElement - the element to get the dimension of

Returns:

the dimension of the basis element within the chain complex

getFiltrationIndex

public int getFiltrationIndex(Simplex basisElement)

Description copied from interface: AbstractFilteredStream

This function returns the filtration index of the requested basis element.

Specified by:

getFiltrationIndex in interface AbstractFilteredStream<Simplex>

Parameters:

basisElement - the basis element to get the filtration index for

Returns:

the filtration index of the specified basis element

getFiltrationValue

public double getFiltrationValue(Simplex basisElement)

Specified by:

getFiltrationValue in interface AbstractFilteredStream<Simplex>

containsElement

public boolean containsElement(Simplex basisElement)

Description copied from interface: AbstractFilteredStream

This function returns whether an element is contained in the stream.

Specified by:

containsElement in interface AbstractFilteredStream<Simplex>

Parameters:

basisElement - the basis element to be tested

getMaximumFiltrationIndex

public int getMaximumFiltrationIndex()

Description copied from interface: AbstractFilteredStream

This function gets the maximum filtration index in the complex.

Specified by:

getMaximumFiltrationIndex in interface AbstractFilteredStream<Simplex>

Returns:

the maximum filtration index

getMinimumFiltrationIndex

public int getMinimumFiltrationIndex()

Description copied from interface: AbstractFilteredStream

This function gets the minimum filtration index in the complex.

Specified by:

getMinimumFiltrationIndex in interface AbstractFilteredStream<Simplex>

Returns:

the minimum filtration index

getSize

public int getSize()

Description copied from interface: AbstractFilteredStream

This function returns the total number of elements in the stream.

Specified by:

getSize in interface AbstractFilteredStream<Simplex>

Returns:

the size of the stream

isFinalized

public boolean isFinalized()

Description copied from interface: AbstractFilteredStream

This function checks whether the finalize() function has been called.

Specified by:

isFinalized in interface AbstractFilteredStream<Simplex>

Returns:

true if the stream has been finalized, and false otherwise

iterator

public java.util.Iterator<Simplex> iterator()

Specified by:

iterator in interface java.lang.Iterable<Simplex>

getBasisComparator

public java.util.Comparator<Simplex> getBasisComparator()

Description copied from interface: AbstractFilteredStream

This function returns a comparator on the underlying basis type.

Specified by:

getBasisComparator in interface AbstractFilteredStream<Simplex>

Returns:

a comparator on the underlying basis type

transform

public <G> PersistenceInvariantDescriptor<Interval<java.lang.Double>,G> transform(PersistenceInvariantDescriptor<Interval<java.lang.Integer>,G> barcodeCollection)

Description copied from interface: AbstractFilteredStream

This function transforms the given collection of filtration index barcodes into filtration value barcodes.

Specified by:

transform in interface AbstractFilteredStream<Simplex>

Parameters:

barcodeCollection - the set of filtration index barcodes

Returns:

the barcodes transformed into filtration value form