Index (JavaPermutationTools - A Java library for computation on permutations)

A B C D E G H I K L M N O P R S T
All Classes All Packages

A

AcyclicEdgeDistance - Class in org.cicirello.permutations.distance: Acyclic Edge Distance:
AcyclicEdgeDistance() - Constructor for class org.cicirello.permutations.distance.AcyclicEdgeDistance: Constructs the distance measurer as specified in the class documentation.

B

BlockInterchangeDistance - Class in org.cicirello.permutations.distance: Block Interchange Distance:
BlockInterchangeDistance() - Constructor for class org.cicirello.permutations.distance.BlockInterchangeDistance: Constructs the distance measurer as specified in the class documentation.

C

copy() - Method in class org.cicirello.permutations.Permutation: Creates an identical copy of this object.
cycle(int[]) - Method in class org.cicirello.permutations.Permutation: Creates a permutation cycle from a sequence of permutation indexes.
CyclicEdgeDistance - Class in org.cicirello.permutations.distance: Cyclic Edge Distance:
CyclicEdgeDistance() - Constructor for class org.cicirello.permutations.distance.CyclicEdgeDistance: Constructs the distance measurer as specified in the class documentation.
CyclicIndependentDistance - Class in org.cicirello.permutations.distance: This class implements the concept of a cyclic independent distance measure.
CyclicIndependentDistance(PermutationDistanceMeasurer) - Constructor for class org.cicirello.permutations.distance.CyclicIndependentDistance: Constructs a distance measure for measuring distance with cyclic independence, such that distance = min_{i in [0,N)} distance(p1,rotate(p2,i))
CyclicIndependentDistanceDouble - Class in org.cicirello.permutations.distance: This class implements the concept of a cyclic independent distance measure.
CyclicIndependentDistanceDouble(PermutationDistanceMeasurerDouble) - Constructor for class org.cicirello.permutations.distance.CyclicIndependentDistanceDouble: Constructs a distance measure for measuring distance with cyclic independence, such that distance = min_{i in [0,N)} distance(p1,rotate(p2,i))
CyclicReversalIndependentDistance - Class in org.cicirello.permutations.distance: This class implements the combination of cyclic independence and reversal independence.
CyclicReversalIndependentDistance(PermutationDistanceMeasurer) - Constructor for class org.cicirello.permutations.distance.CyclicReversalIndependentDistance: Constructs a distance measure for measuring distance with cyclic and reversal independence, such that distance = min_{i in [0,N)} { distance(p1,rotate(p2,i)), distance(p1,rotate(reverse(p2),i)) }
CyclicReversalIndependentDistanceDouble - Class in org.cicirello.permutations.distance: This class implements the combination of cyclic independence and reversal independence.
CyclicReversalIndependentDistanceDouble(PermutationDistanceMeasurerDouble) - Constructor for class org.cicirello.permutations.distance.CyclicReversalIndependentDistanceDouble: Constructs a distance measure for measuring distance with cyclic and reversal independence, such that distance = min_{i in [0,N)} { distance(p1,rotate(p2,i)), distance(p1,rotate(reverse(p2),i)) }
CyclicRTypeDistance - Class in org.cicirello.permutations.distance: Cyclic RType Distance:
CyclicRTypeDistance() - Constructor for class org.cicirello.permutations.distance.CyclicRTypeDistance: Constructs the distance measurer as specified in the class documentation.

D

DeviationDistance - Class in org.cicirello.permutations.distance: Deviation Distance:
DeviationDistance() - Constructor for class org.cicirello.permutations.distance.DeviationDistance: Constructs the distance measurer as specified in the class documentation.
DeviationDistanceNormalized - Class in org.cicirello.permutations.distance: Normalized Deviation Distance:
DeviationDistanceNormalized() - Constructor for class org.cicirello.permutations.distance.DeviationDistanceNormalized: Constructs the distance measurer as specified in the class documentation.
DeviationDistanceNormalized2005 - Class in org.cicirello.permutations.distance: Normalized Deviation Distance:
DeviationDistanceNormalized2005() - Constructor for class org.cicirello.permutations.distance.DeviationDistanceNormalized2005: Constructs the distance measurer as specified in the class documentation.
distance(boolean[], boolean[]) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two arrays.
distance(boolean[], boolean[]) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(boolean[], boolean[]) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two arrays.
distance(boolean[], boolean[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two arrays.
distance(byte[], byte[]) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two arrays.
distance(byte[], byte[]) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(byte[], byte[]) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two arrays.
distance(byte[], byte[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two arrays.
distance(char[], char[]) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two arrays.
distance(char[], char[]) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(char[], char[]) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two arrays.
distance(char[], char[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two arrays.
distance(double[], double[]) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two arrays.
distance(double[], double[]) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(double[], double[]) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two arrays.
distance(double[], double[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two arrays.
distance(float[], float[]) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two arrays.
distance(float[], float[]) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(float[], float[]) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two arrays.
distance(float[], float[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two arrays.
distance(int[], int[]) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two arrays.
distance(int[], int[]) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(int[], int[]) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two arrays.
distance(int[], int[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two arrays.
distance(long[], long[]) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two arrays.
distance(long[], long[]) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(long[], long[]) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two arrays.
distance(long[], long[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two arrays.
distance(short[], short[]) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two arrays.
distance(short[], short[]) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(short[], short[]) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two arrays.
distance(short[], short[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two arrays.
distance(Object[], Object[]) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two arrays of objects.
distance(Object[], Object[]) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(Object[], Object[]) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two arrays of objects.
distance(Object[], Object[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two arrays of objects.
distance(String, String) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two Strings.
distance(String, String) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(String, String) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two Strings.
distance(String, String) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two Strings.
distance(List<T>, List<T>) - Method in class org.cicirello.sequences.distance.EditDistance: Measures the distance between two lists of objects.
distance(List<T>, List<T>) - Method in class org.cicirello.sequences.distance.ExactMatchDistance
distance(List<T>, List<T>) - Method in class org.cicirello.sequences.distance.KendallTauSequenceDistance: Measures the distance between two lists of objects.
distance(List<T>, List<T>) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer: Measures the distance between two lists of objects.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.AcyclicEdgeDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.BlockInterchangeDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.CyclicEdgeDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.CyclicIndependentDistance: Measures the distance between two permutations, with cyclic independence: distance = min_{i in [0,N)} distance(p1,rotate(p2,i))
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.CyclicReversalIndependentDistance: Measures the distance between two permutations, with cyclic and reversal independence: distance = min_{i in [0,N)} { distance(p1,rotate(p2,i)), distance(p1,rotate(reverse(p2),i)) }
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.CyclicRTypeDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.DeviationDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.ExactMatchDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.InterchangeDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.KendallTauDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.LeeDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in interface org.cicirello.permutations.distance.PermutationDistanceMeasurer: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.ReinsertionDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.ReversalDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.ReversalIndependentDistance: Measures the distance between two permutations, with reversal independence: distance = min { distance(p1,p2), distance(p1,reverse(p2)) }
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.RTypeDistance: Measures the distance between two permutations.
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.ScrambleDistance
distance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.SquaredDeviationDistance: Measures the distance between two permutations.
distancef(boolean[], boolean[]) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(boolean[], boolean[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(boolean[], boolean[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two arrays.
distancef(byte[], byte[]) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(byte[], byte[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(byte[], byte[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two arrays.
distancef(char[], char[]) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(char[], char[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(char[], char[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two arrays.
distancef(double[], double[]) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(double[], double[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(double[], double[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two arrays.
distancef(float[], float[]) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(float[], float[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(float[], float[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two arrays.
distancef(int[], int[]) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(int[], int[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(int[], int[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two arrays.
distancef(long[], long[]) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(long[], long[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(long[], long[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two arrays.
distancef(short[], short[]) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(short[], short[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(short[], short[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two arrays.
distancef(Object[], Object[]) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(Object[], Object[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(Object[], Object[]) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two arrays of objects.
distancef(String, String) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(String, String) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(String, String) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two Strings.
distancef(List<T>, List<T>) - Method in class org.cicirello.sequences.distance.EditDistance
distancef(List<T>, List<T>) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurer
distancef(List<T>, List<T>) - Method in interface org.cicirello.sequences.distance.SequenceDistanceMeasurerDouble: Measures the distance between two lists of objects.
distancef(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.CyclicIndependentDistanceDouble: Measures the distance between two permutations, with cyclic independence: distance = min_{i in [0,N)} distance(p1,rotate(p2,i))
distancef(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.CyclicReversalIndependentDistanceDouble: Measures the distance between two permutations, with cyclic and reversal independence: distance = min_{i in [0,N)} { distance(p1,rotate(p2,i)), distance(p1,rotate(reverse(p2),i)) }
distancef(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.DeviationDistanceNormalized: Measures the distance between two permutations
distancef(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.DeviationDistanceNormalized2005: Measures the distance between two permutations
distancef(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.EditDistance: Measures the distance between two permutations.
distancef(Permutation, Permutation) - Method in interface org.cicirello.permutations.distance.PermutationDistanceMeasurer: Measures the distance between two permutations
distancef(Permutation, Permutation) - Method in interface org.cicirello.permutations.distance.PermutationDistanceMeasurerDouble: Measures the distance between two permutations
distancef(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.ReversalIndependentDistanceDouble: Measures the distance between two permutations, with reversal independence: distance = min { distance(p1,p2), distance(p1,reverse(p2)) }

E

EditDistance - Class in org.cicirello.permutations.distance: Edit Distance:
EditDistance - Class in org.cicirello.sequences.distance: EditDistance is an implementation of Wagner and Fischer's dynamic programming algorithm for computing string edit distance.
EditDistance() - Constructor for class org.cicirello.permutations.distance.EditDistance: Default edit distance computes number of remove and reinsert operations to transform one permutation into the other.
EditDistance(double, double, double) - Constructor for class org.cicirello.permutations.distance.EditDistance: Constructs an EditDistance function.
EditDistance(double, double, double) - Constructor for class org.cicirello.sequences.distance.EditDistance: Constructs an edit distance measure with the specified edit operation costs.
EditDistance(int, int, int) - Constructor for class org.cicirello.sequences.distance.EditDistance: Constructs an edit distance measure with the specified edit operation costs.
equals(Object) - Method in class org.cicirello.permutations.Permutation: Equality test: Two permutations are equal if they are of the same length and contain the same elements in the same order.
ExactMatchDistance - Class in org.cicirello.permutations.distance: Exact Match Distance:
ExactMatchDistance - Class in org.cicirello.sequences.distance: ExactMatch distance (or Hamming Distance) of a pair of non-binary strings (or more generally sequences) is the number of sequence (or string) positions where the two sequences differ.
ExactMatchDistance() - Constructor for class org.cicirello.permutations.distance.ExactMatchDistance: Constructs the distance measurer as specified in the class documentation.
ExactMatchDistance() - Constructor for class org.cicirello.sequences.distance.ExactMatchDistance: Constructs the distance measurer as specified in the class documentation.

G

get(int) - Method in class org.cicirello.permutations.Permutation: Retrieves the i'th integer of the permutation.
get(int, int) - Method in class org.cicirello.permutations.Permutation: Retrieves a range of elements from the permutation.
get(int, int, int[]) - Method in class org.cicirello.permutations.Permutation: Retrieves a range of elements from the permutation.
getInverse() - Method in class org.cicirello.permutations.Permutation: Computes the inverse of the permutation.
getInversePermutation() - Method in class org.cicirello.permutations.Permutation: Computes a Permutation that is the inverse of this Permutation.

H

hashCode() - Method in class org.cicirello.permutations.Permutation: Uses Java's Arrays class's method for generating a hashCode from an array of ints.
hasNext() - Method in class org.cicirello.permutations.PermutationIterator

I

InterchangeDistance - Class in org.cicirello.permutations.distance: Interchange Distance:
InterchangeDistance() - Constructor for class org.cicirello.permutations.distance.InterchangeDistance: Constructs the distance measurer as specified in the class documentation.
invert() - Method in class org.cicirello.permutations.Permutation: Inverts the Permutation, such that if p1 is the Permutation immediately prior to the call to invert, and if p2 is the Permutation immediately after the call to invert, then p1.get(i) == j iff p2.get(j) == i, for all i, j.
iterator() - Method in class org.cicirello.permutations.Permutation: Returns an Iterator over all Permutations the length of this Permutation.

K

KendallTauDistance - Class in org.cicirello.permutations.distance: Kendall Tau Distance:
KendallTauDistance() - Constructor for class org.cicirello.permutations.distance.KendallTauDistance: Constructs the distance measurer as specified in the class documentation.
KendallTauSequenceDistance - Class in org.cicirello.sequences.distance: Kendall Tau Sequence Distance is the minimum number of adjacent swaps necessary to transform one sequence into the other.
KendallTauSequenceDistance() - Constructor for class org.cicirello.sequences.distance.KendallTauSequenceDistance: The KendallTauDistance class provides two algorithms.
KendallTauSequenceDistance(boolean) - Constructor for class org.cicirello.sequences.distance.KendallTauSequenceDistance: The KendallTauDistance class provides two algorithms.

L

LeeDistance - Class in org.cicirello.permutations.distance: Lee Distance:
LeeDistance() - Constructor for class org.cicirello.permutations.distance.LeeDistance: Constructs the distance measurer as specified in the class documentation.
length() - Method in class org.cicirello.permutations.Permutation: Retrieves the length of the permutation.
LongestCommonSubsequenceDistance - Class in org.cicirello.sequences.distance: LongestCommonSubsequenceDistance is a form of EditDistance, where the edit operations are limited to deletions and insertions (i.e., no replacements or changes), and where the cost of an edit operation is simply 1.
LongestCommonSubsequenceDistance() - Constructor for class org.cicirello.sequences.distance.LongestCommonSubsequenceDistance: Constructs a longest common subsequence distance.

M

max(int) - Method in class org.cicirello.permutations.distance.AcyclicEdgeDistance
max(int) - Method in class org.cicirello.permutations.distance.BlockInterchangeDistance
max(int) - Method in class org.cicirello.permutations.distance.CyclicEdgeDistance
max(int) - Method in class org.cicirello.permutations.distance.CyclicRTypeDistance
max(int) - Method in class org.cicirello.permutations.distance.DeviationDistance
max(int) - Method in class org.cicirello.permutations.distance.ExactMatchDistance
max(int) - Method in class org.cicirello.permutations.distance.InterchangeDistance
max(int) - Method in class org.cicirello.permutations.distance.KendallTauDistance
max(int) - Method in class org.cicirello.permutations.distance.LeeDistance
max(int) - Method in interface org.cicirello.permutations.distance.NormalizedPermutationDistanceMeasurer: Computes the maximum possible distance between permutations of a specified length.
max(int) - Method in class org.cicirello.permutations.distance.ReinsertionDistance
max(int) - Method in class org.cicirello.permutations.distance.ReversalDistance: Computes the maximum possible distance between permutations of a specified length.
max(int) - Method in class org.cicirello.permutations.distance.RTypeDistance
max(int) - Method in class org.cicirello.permutations.distance.ScrambleDistance
max(int) - Method in class org.cicirello.permutations.distance.SquaredDeviationDistance
maxf(int) - Method in class org.cicirello.permutations.distance.DeviationDistanceNormalized
maxf(int) - Method in class org.cicirello.permutations.distance.DeviationDistanceNormalized2005
maxf(int) - Method in interface org.cicirello.permutations.distance.NormalizedPermutationDistanceMeasurer
maxf(int) - Method in interface org.cicirello.permutations.distance.NormalizedPermutationDistanceMeasurerDouble: Computes the maximum possible distance between permutations of a specified length.
Mechanic() - Constructor for class org.cicirello.permutations.Permutation.Mechanic: The default constructor can only be called by subclasses.

N

next() - Method in class org.cicirello.permutations.PermutationIterator
normalizedDistance(Permutation, Permutation) - Method in class org.cicirello.permutations.distance.DeviationDistanceNormalized2005: Measures the distance between two permutations, normalized to the interval [0.0, 1.0].
normalizedDistance(Permutation, Permutation) - Method in interface org.cicirello.permutations.distance.NormalizedPermutationDistanceMeasurer: Measures the distance between two permutations, normalized to the interval [0.0, 1.0].
normalizedDistance(Permutation, Permutation) - Method in interface org.cicirello.permutations.distance.NormalizedPermutationDistanceMeasurerDouble: Measures the distance between two permutations, normalized to the interval [0.0, 1.0].
NormalizedPermutationDistanceMeasurer - Interface in org.cicirello.permutations.distance: Implement this interface to define a distance metric for permutations that supports normalizing the distance to the interval [0,1], but where the base distance is an integer value.
NormalizedPermutationDistanceMeasurerDouble - Interface in org.cicirello.permutations.distance: Implement this interface to define a distance metric for permutations that supports normalizing the distance to the interval [0,1].

O

org.cicirello.jpt - module org.cicirello.jpt: JavaPermutationTools - A Java library for computation on permutations
org.cicirello.permutations - package org.cicirello.permutations: Collection of classes related to representing and manipulating permutations.
org.cicirello.permutations.distance - package org.cicirello.permutations.distance: Implementations of a variety of permutation distance measures.
org.cicirello.sequences - package org.cicirello.sequences: Classes that perform a variety of operations on sequences (such as arrays, etc).
org.cicirello.sequences.distance - package org.cicirello.sequences.distance: Implementations of distance measures for general sequences of various forms, including Strings, arrays of primitive types, arrays of objects, etc.

P

Permutation - Class in org.cicirello.permutations: Representation of a permutation of the integers from 0 to N-1, inclusive.
Permutation(int) - Constructor for class org.cicirello.permutations.Permutation: Initializes a random permutation of n integers.
Permutation(int[]) - Constructor for class org.cicirello.permutations.Permutation: Initializes a permutation of n integers to be identical to the elements of an array.
Permutation(int, int) - Constructor for class org.cicirello.permutations.Permutation: Initializes a specific permutation from an integer in mixed radix form representing the chosen permutation.
Permutation(int, BigInteger) - Constructor for class org.cicirello.permutations.Permutation: Initializes a specific permutation from an integer in mixed radix form representing the chosen permutation.
Permutation(int, Random) - Constructor for class org.cicirello.permutations.Permutation: Initializes a random permutation of n integers.
Permutation(int, SplittableRandom) - Constructor for class org.cicirello.permutations.Permutation: Initializes a random permutation of n integers.
Permutation(Permutation) - Constructor for class org.cicirello.permutations.Permutation: Initializes a permutation of n integers to be identical to a given permutation.
Permutation(Permutation, int) - Constructor for class org.cicirello.permutations.Permutation: Initializes a permutation of the integers in the interval [0, length) based on their relative order in a permutation p.
Permutation.Mechanic - Class in org.cicirello.permutations: The Permutation.Mechanic class provides a means of adding application-specific operations on Permutations without the need to directly alter the Permutation class.
PermutationDistanceMeasurer - Interface in org.cicirello.permutations.distance: Implement this interface, PermutationDistanceMeasurer, to define a distance metric for permutations.
PermutationDistanceMeasurerDouble - Interface in org.cicirello.permutations.distance: Implement this interface, PermutationDistanceMeasurerDouble, to define a distance metric for permutations, where the distance is a floating-point value.
PermutationIterator - Class in org.cicirello.permutations: Iterator over all permutations of a specified length, n, of the integers in the interval [0,n).
PermutationIterator(int) - Constructor for class org.cicirello.permutations.PermutationIterator: Initializes a PermutationIterator to iterate over all permutations of a given length.
PermutationIterator(Permutation) - Constructor for class org.cicirello.permutations.PermutationIterator: Initializes a PermutationIterator to iterate over all permutations the same length as a given permutation.

R

ReinsertionDistance - Class in org.cicirello.permutations.distance: Reinsertion Distance:
ReinsertionDistance() - Constructor for class org.cicirello.permutations.distance.ReinsertionDistance: Constructs the distance measurer as specified in the class documentation.
removeAndInsert(int, int) - Method in class org.cicirello.permutations.Permutation: Removes integer from one position and then inserts it into a a new position shifting the rest of the permutation as necessary.
removeAndInsert(int, int, int) - Method in class org.cicirello.permutations.Permutation: Removes a sub-array of integers from one position and then inserts it into a a new position shifting the rest of the permutation as necessary.
ReversalDistance - Class in org.cicirello.permutations.distance: Reversal Distance:
ReversalDistance() - Constructor for class org.cicirello.permutations.distance.ReversalDistance: Construct the distance measure.
ReversalDistance(int) - Constructor for class org.cicirello.permutations.distance.ReversalDistance: Defines a distance measure for permutations of length n.
ReversalIndependentDistance - Class in org.cicirello.permutations.distance: This class implements the concept of a reversal independent distance measure.
ReversalIndependentDistance(PermutationDistanceMeasurer) - Constructor for class org.cicirello.permutations.distance.ReversalIndependentDistance: Constructs a distance measure for measuring distance with reversal independence, such that distance = min { distance(p1,p2), distance(p1,reverse(p2)) }
ReversalIndependentDistanceDouble - Class in org.cicirello.permutations.distance: This class implements the concept of a reversal independent distance measure.
ReversalIndependentDistanceDouble(PermutationDistanceMeasurerDouble) - Constructor for class org.cicirello.permutations.distance.ReversalIndependentDistanceDouble: Constructs a distance measure for measuring distance with reversal independence, such that distance = min { distance(p1,p2), distance(p1,reverse(p2)) }
reverse() - Method in class org.cicirello.permutations.Permutation: Reverses the order of the elements in the permutation.
reverse(int, int) - Method in class org.cicirello.permutations.Permutation: Reverses the order of the elements of a subrange of the permutation.
rotate(int) - Method in class org.cicirello.permutations.Permutation: Circular rotation of permutation (to the left).
RTypeDistance - Class in org.cicirello.permutations.distance: RType Distance:
RTypeDistance() - Constructor for class org.cicirello.permutations.distance.RTypeDistance: Constructs the distance measurer as specified in the class documentation.

S

sample(byte[], double) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample, without replacement, from a given source array with a specified probability of an element's inclusion in the sample.
sample(byte[], int, byte[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sample(char[], double) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample, without replacement, from a given source array with a specified probability of an element's inclusion in the sample.
sample(char[], int, char[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sample(double[], double) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample, without replacement, from a given source array with a specified probability of an element's inclusion in the sample.
sample(double[], int, double[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sample(float[], double) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample, without replacement, from a given source array with a specified probability of an element's inclusion in the sample.
sample(float[], int, float[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sample(int[], double) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample, without replacement, from a given source array with a specified probability of an element's inclusion in the sample.
sample(int[], int, int[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sample(long[], double) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample, without replacement, from a given source array with a specified probability of an element's inclusion in the sample.
sample(long[], int, long[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sample(short[], double) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample, without replacement, from a given source array with a specified probability of an element's inclusion in the sample.
sample(short[], int, short[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sample(String, double) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample, without replacement, from a given String with a specified probability of a character's inclusion in the sample.
sample(String, int, char[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k chars, without replacement, from a given source String.
sample(T[], double) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample, without replacement, from a given source array with a specified probability of an element's inclusion in the sample.
sample(T[], int, T[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleInsertion(byte[], int, byte[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleInsertion(char[], int, char[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleInsertion(double[], int, double[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleInsertion(float[], int, float[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleInsertion(int[], int, int[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleInsertion(long[], int, long[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleInsertion(short[], int, short[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleInsertion(String, int, char[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k chars, without replacement, from a given source String.
sampleInsertion(T[], int, T[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
samplePool(byte[], int, byte[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
samplePool(char[], int, char[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
samplePool(double[], int, double[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
samplePool(float[], int, float[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
samplePool(int[], int, int[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
samplePool(long[], int, long[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
samplePool(short[], int, short[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
samplePool(String, int, char[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k chars, without replacement, from a given source String.
samplePool(T[], int, T[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleReservoir(byte[], int, byte[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleReservoir(char[], int, char[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleReservoir(double[], int, double[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleReservoir(float[], int, float[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleReservoir(int[], int, int[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleReservoir(long[], int, long[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleReservoir(short[], int, short[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
sampleReservoir(String, int, char[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k chars, without replacement, from a given source String.
sampleReservoir(T[], int, T[]) - Static method in class org.cicirello.sequences.SequenceSampler: Generates a random sample of k elements, without replacement, from a given source array.
scramble() - Method in class org.cicirello.permutations.Permutation: Randomly shuffles the permutation.
scramble(boolean) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles the permutation.
scramble(int[]) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles a non-contiguous set of permutation elements.
scramble(int[], Random) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles a non-contiguous set of permutation elements.
scramble(int[], SplittableRandom) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles a non-contiguous set of permutation elements.
scramble(int, int) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles a segment.
scramble(int, int, Random) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles a segment.
scramble(int, int, SplittableRandom) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles a segment.
scramble(Random) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles the permutation.
scramble(Random, boolean) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles the permutation.
scramble(SplittableRandom) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles the permutation.
scramble(SplittableRandom, boolean) - Method in class org.cicirello.permutations.Permutation: Randomly shuffles the permutation.
ScrambleDistance - Class in org.cicirello.permutations.distance: Scramble Distance:
ScrambleDistance() - Constructor for class org.cicirello.permutations.distance.ScrambleDistance: Constructs the distance measurer as specified in the class documentation.
SequenceDistanceMeasurer - Interface in org.cicirello.sequences.distance: Implement this interface, SequenceDistanceMeasurer, to define a distance metric for sequences.
SequenceDistanceMeasurerDouble - Interface in org.cicirello.sequences.distance: Implement this interface, SequenceDistanceMeasurerDouble, to define a distance metric for sequences.
SequenceSampler - Class in org.cicirello.sequences: ArraySampler is a class of utility methods related to efficiently generating random samples of array elements, without replacement.
set(int[]) - Method in class org.cicirello.permutations.Permutation: Changes the state of this permutation to be identical to the elements of an array.
set(Permutation, int[]) - Method in class org.cicirello.permutations.Permutation.Mechanic: Changes the state of the Permutation according to the contents of an array of int values.
set(Permutation, int[], int, int, int) - Method in class org.cicirello.permutations.Permutation.Mechanic: Changes a range of permutation elements.
set(Permutation, int, int) - Method in class org.cicirello.permutations.Permutation.Mechanic: Changes the integer in one specific location of a Permutation.
set(Permutation, int, int[]) - Method in class org.cicirello.permutations.Permutation.Mechanic: Changes a range of permutation elements.
SquaredDeviationDistance - Class in org.cicirello.permutations.distance: Squared Deviation Distance:
SquaredDeviationDistance() - Constructor for class org.cicirello.permutations.distance.SquaredDeviationDistance: Constructs the distance measurer as specified in the class documentation.
swap(int, int) - Method in class org.cicirello.permutations.Permutation: Swaps 2 integers in the permutation.
swapBlocks(int, int, int, int) - Method in class org.cicirello.permutations.Permutation: Swaps 2 non-overlapping blocks, where a block is a subsequence.

T

toArray() - Method in class org.cicirello.permutations.Permutation: Generates an array of int values from the interval [0, n) in the same order that they occur in this Permutation.
toArray(int[]) - Method in class org.cicirello.permutations.Permutation: Generates an array of int values from the interval [0, n) in the same order that they occur in this Permutation.
toBigInteger() - Method in class org.cicirello.permutations.Permutation: Generates a unique integer representing the permutation.
toInteger() - Method in class org.cicirello.permutations.Permutation: Generates a unique integer representing the permutation.
toString() - Method in class org.cicirello.permutations.Permutation: Creates a String representing the permutation.

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