Class 
Description 
AcyclicEdgeDistance 
Acyclic Edge Distance:

BlockInterchangeDistance 
Block Interchange Distance:

Copyable<T extends Copyable<T>> 
A simple interface for objects that can be copied.

CyclicEdgeDistance 
Cyclic Edge Distance:

CyclicIndependentDistance 
This class implements the concept of a cyclic independent distance measure.

CyclicIndependentDistanceDouble 
This class implements the concept of a cyclic independent distance measure.

CyclicReversalIndependentDistance 
This class implements the combination of cyclic independence and reversal independence.

CyclicReversalIndependentDistanceDouble 
This class implements the combination of cyclic independence and reversal independence.

CyclicRTypeDistance 
Cyclic RType Distance:

DeviationDistance 
Deviation Distance:

DeviationDistanceNormalized 
Normalized Deviation Distance:

DeviationDistanceNormalized2005 
Normalized Deviation Distance:

EditDistance 
Edit Distance:

EditDistance 
EditDistance is an implementation of Wagner and Fischer's dynamic programming algorithm for computing string edit distance.

ExactMatchDistance 
Exact Match Distance:

ExactMatchDistance 
ExactMatch distance (or Hamming Distance) of a pair of nonbinary strings (or more generally sequences) is the number of
sequence (or string) positions where the two sequences differ.

InterchangeDistance 
Interchange Distance:

JacobiDiagonalization 
This class uses Jacobi iteration to compute the eigenvalues and eigenvectors of a symmetric matrix, provided as a 2D Java array.

KendallTauDistance 
Kendall Tau Distance:

KendallTauSequenceDistance 
Kendall Tau Sequence Distance is
the minimum number of adjacent swaps necessary to transform one sequence into the other.

LeeDistance 
Lee Distance:

LongestCommonSubsequenceDistance 
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.

MathFunctions 
MathFunctions is a class of utility methods that implement various mathematical functions.

MatrixOps 
Utility class of basic linear algebra matrix operations, where matrices are
represented as 2D Java arrays.

NormalizedPermutationDistanceMeasurer 
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 
Implement this interface to define a distance metric for permutations that supports
normalizing the distance to the interval [0,1].

Permutation 
Representation of a permutation of the integers from 0 to N1, inclusive.

Permutation.Mechanic 
The Permutation.Mechanic class provides a means of adding applicationspecific
operations on Permutations without the need to directly alter the Permutation
class.

PermutationDistanceMeasurer 
Implement this interface, PermutationDistanceMeasurer, to define a distance metric for permutations.

PermutationDistanceMeasurerDouble 
Implement this interface, PermutationDistanceMeasurerDouble, to define a distance metric for permutations,
where the distance is a floatingpoint value.

PermutationIterator 
Iterator over all permutations of a specified length, n, of the integers in the interval [0,n).

RandomIndexer 
RandomIndexer is a class of utility methods related to
efficiently generating random indexes, and combination of indexes, into arrays.

RandomVariates 
This utility class provides methods for generating random variates from
different distributions.

ReinsertionDistance 
Reinsertion Distance:

ReversalDistance 
Reversal Distance:

ReversalIndependentDistance 
This class implements the concept of a reversal independent distance measure.

ReversalIndependentDistanceDouble 
This class implements the concept of a reversal independent distance measure.

RTypeDistance 
RType Distance:

ScrambleDistance 
Scramble Distance:

SequenceDistanceMeasurer 
Implement this interface, SequenceDistanceMeasurer, to define a distance metric for sequences.

SequenceDistanceMeasurerDouble 
Implement this interface, SequenceDistanceMeasurerDouble, to define a distance metric for sequences.

SequenceSampler 
ArraySampler is a class of utility methods related to
efficiently generating random samples of array elements, without replacement.

SquaredDeviationDistance 
Squared Deviation Distance:

Statistics 
Utility class of basic statistics.
