edu.stanford.math.plex4.streams.impl

Class ExplicitStream<T extends PrimitiveBasisElement>

java.lang.Object

edu.stanford.math.plex4.streams.interfaces.PrimitiveStream<T>

edu.stanford.math.plex4.streams.impl.ExplicitStream<T>

All Implemented Interfaces:

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

Direct Known Subclasses:

ExplicitCellStream, ExplicitSimplexStream, WitnessBicomplex

public class ExplicitStream<T extends PrimitiveBasisElement>
extends PrimitiveStream<T>

This class implements the functionality of a user-defined filtered chain complex. It derives from the PrimitiveStream class, meaning that it underlying basis type must be a geometric primitive.

Author:

Andrew Tausz

Field Summary

Fields inherited from class edu.stanford.math.plex4.streams.interfaces.PrimitiveStream

storageStructure

Constructor Summary

Constructors

Constructor and Description
ExplicitStream(AbstractFilteredStream<T> stream, java.util.Comparator<T> comparator) This constructor initializes the stream from an existing stream.
ExplicitStream(java.util.Comparator<T> comparator) Constructor which accepts a comparator for comparing the type T.
ExplicitStream(java.util.Comparator<T> comparator, double maxFiltrationValue)

Method Summary

Methods

Modifier and Type	Method and Description
void	addAllElements(AbstractFilteredStream<T> stream) This function copies all of the elements in the supplied stream to the current one.
void	addElement(T basisElement, double filtrationValue) This function adds a basis element the stream with specified filtration index.
protected void	constructComplex() This abstract function performs the construction of the filtered chain complex.
boolean	containsElement(T basisElement) This function returns true if the stream contains the query element.
void	ensureAllFaces() This function ensures that all of the faces of the all of the elements are present in the stream.
double	getFiltrationValue(T basisElement)
boolean	removeElementIfPresent(T basisElement) This function removes the specified element from the stream.
<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 edu.stanford.math.plex4.streams.interfaces.PrimitiveStream

finalizeStream, getBasisComparator, getBoundary, getBoundaryCoefficients, getDimension, getFiltrationIndex, getMaximumFiltrationIndex, getMinimumFiltrationIndex, getSize, isFinalized, iterator, validate, validateVerbose

Methods inherited from class java.lang.Object

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

Constructor Detail

ExplicitStream

public ExplicitStream(java.util.Comparator<T> comparator)

Constructor which accepts a comparator for comparing the type T. This comparator defines the ordering on the type T. Thus the overall filtered objects are sorted first in order of filtration, and then by the ordering provided by the comparator.

Parameters:

comparator - a Comparator which provides an ordering of the objects

ExplicitStream

public ExplicitStream(java.util.Comparator<T> comparator,
              double maxFiltrationValue)

ExplicitStream

public ExplicitStream(AbstractFilteredStream<T> stream,
              java.util.Comparator<T> comparator)

This constructor initializes the stream from an existing stream. It copies all of the elements of the supplied stream to the current one.

Parameters:

stream - the stream to copy from

comparator - a Comparator which provides an ordering on the basis elements

Method Detail

addAllElements

public void addAllElements(AbstractFilteredStream<T> stream)

This function copies all of the elements in the supplied stream to the current one.

Parameters:

stream - the stream to copy from

addElement

public void addElement(T basisElement,
              double filtrationValue)

This function adds a basis element the stream with specified filtration index.

Parameters:

basisElement - the basis element to add

filtrationIndex - the filtration index of the basis element

removeElementIfPresent

public boolean removeElementIfPresent(T basisElement)

This function removes the specified element from the stream. In the case that the element is not present, this function does not do anything.

Parameters:

basisElement - the element to remove.

Returns:

true if the element was found and removed, and false otherwise

containsElement

public boolean containsElement(T basisElement)

This function returns true if the stream contains the query element.

Specified by:

containsElement in interface AbstractFilteredStream<T extends PrimitiveBasisElement>

Overrides:

containsElement in class PrimitiveStream<T extends PrimitiveBasisElement>

Parameters:

basisElement - the element to find

Returns:

true if the element is in the stream and false otherwise

constructComplex

protected void constructComplex()

Description copied from class: PrimitiveStream

This abstract function performs the construction of the filtered chain complex. For example, this might construct the complex from a metric space via a Vietoris-Rips or witness construction.

Specified by:

constructComplex in class PrimitiveStream<T extends PrimitiveBasisElement>

ensureAllFaces

public void ensureAllFaces()

This function ensures that all of the faces of the all of the elements are present in the stream. It adds the missing faces with filtration indices that are consistent. In other words, it ensures that the filtration indices of an element equals the minimum filtration index of its cofaces.

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.

Parameters:

barcodeCollection - the set of filtration index barcodes

Returns:

the barcodes transformed into filtration value form

getFiltrationValue

public double getFiltrationValue(T basisElement)