All Classes

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 non-binary 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 2-D 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 2-D 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 N-1, inclusive.
Permutation.Mechanic	The Permutation.Mechanic class provides a means of adding application-specific 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 floating-point 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.