edu.stanford.math.plex4.homology.barcodes

Class BarcodeUtility

java.lang.Object

edu.stanford.math.plex4.homology.barcodes.BarcodeUtility

public class BarcodeUtility
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
BarcodeUtility()

Method Summary

Methods

Modifier and Type	Method and Description
static <G> java.util.List<edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<Interval<java.lang.Double>,G>>	filterIntervalPairsByMinimumLength(java.lang.Iterable<edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<Interval<java.lang.Double>,G>> intervals, double minimumLength) Given a collection of intervals object pairs, this function returns those intervals with length greater than or equal to the minimum specified.
static java.util.List<Interval<java.lang.Double>>	filterIntervalsByMinimumLength(java.lang.Iterable<Interval<java.lang.Double>> intervals, double minimumLength) Given a collection of intervals, this function returns those intervals with length greater than or equal to the minimum specified.
static <G> double[][]	getEndpoints(AnnotatedBarcodeCollection<java.lang.Double,G> collection, int dimension, boolean skipInfiniteIntervals) This function returns an array containing the set of endpoint of the intervals.
static double[][]	getEndpoints(java.util.List<Interval<java.lang.Double>> intervals, int dimension, boolean skipInfiniteIntervals) This function returns an array containing the set of endpoint of the intervals.
static double	getLength(Interval<java.lang.Double> interval)
static <G> java.util.List<edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<Interval<java.lang.Double>,G>>	getLongestAnnotatedBarcodes(java.util.List<edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<Interval<java.lang.Double>,G>> intervals, int k)
static java.util.List<Interval<java.lang.Double>>	getLongestBarcodes(java.util.List<Interval<java.lang.Double>> intervals, int k)

Methods inherited from class java.lang.Object

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

Constructor Detail

BarcodeUtility

public BarcodeUtility()

Method Detail

getEndpoints

public static <G> double[][] getEndpoints(AnnotatedBarcodeCollection<java.lang.Double,G> collection,
                          int dimension,
                          boolean skipInfiniteIntervals)

This function returns an array containing the set of endpoint of the intervals.

Type Parameters:

G -

Parameters:

collection - the barcode collection

dimension - the dimension at which to get the endpoints

skipInfiniteIntervals - boolean flag indicating whether to skip infinite intervals

Returns:

an n x 2 array of doubles containing the endpoints of the intervals

getEndpoints

public static double[][] getEndpoints(java.util.List<Interval<java.lang.Double>> intervals,
                      int dimension,
                      boolean skipInfiniteIntervals)

This function returns an array containing the set of endpoint of the intervals.

Type Parameters:

G -

Parameters:

intervals - the list of intervals

dimension - the dimension at which to get the endpoints

skipInfiniteIntervals - boolean flag indicating whether to skip infinite intervals

Returns:

an n x 2 array of doubles containing the endpoints of the intervals

getLongestBarcodes

public static java.util.List<Interval<java.lang.Double>> getLongestBarcodes(java.util.List<Interval<java.lang.Double>> intervals,
                                                            int k)

getLongestAnnotatedBarcodes

public static <G> java.util.List<edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<Interval<java.lang.Double>,G>> getLongestAnnotatedBarcodes(java.util.List<edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<Interval<java.lang.Double>,G>> intervals,
                                                                                                                                         int k)

getLength

public static double getLength(Interval<java.lang.Double> interval)

filterIntervalsByMinimumLength

public static java.util.List<Interval<java.lang.Double>> filterIntervalsByMinimumLength(java.lang.Iterable<Interval<java.lang.Double>> intervals,
                                                                        double minimumLength)

Given a collection of intervals, this function returns those intervals with length greater than or equal to the minimum specified.

Parameters:

intervals - the set of intervals

minimumLength - the minimum length

Returns:

those intervals longer than minimumLength

filterIntervalPairsByMinimumLength

public static <G> java.util.List<edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<Interval<java.lang.Double>,G>> filterIntervalPairsByMinimumLength(java.lang.Iterable<edu.stanford.math.primitivelib.autogen.pair.ObjectObjectPair<Interval<java.lang.Double>,G>> intervals,
                                                                                                                                                double minimumLength)

Given a collection of intervals object pairs, this function returns those intervals with length greater than or equal to the minimum specified.

Parameters:

intervals - the set of intervals

minimumLength - the minimum length

Returns:

those intervals longer than minimumLength