All Classes Interface Summary Class Summary
Class |
Description |
AcyclicEdgeDistance |
Acyclic Edge Distance:
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BlockInterchangeDistance |
Block Interchange Distance:
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Copyable<T extends Copyable<T>> |
A simple interface for objects that can be copied.
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CyclicEdgeDistance |
Cyclic Edge Distance:
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CyclicIndependentDistance |
This class implements the concept of a cyclic independent distance measure.
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CyclicIndependentDistanceDouble |
This class implements the concept of a cyclic independent distance measure.
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CyclicReversalIndependentDistance |
This class implements the combination of cyclic independence and reversal independence.
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CyclicReversalIndependentDistanceDouble |
This class implements the combination of cyclic independence and reversal independence.
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CyclicRTypeDistance |
Cyclic RType Distance:
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DeviationDistance |
Deviation Distance:
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DeviationDistanceNormalized |
Normalized Deviation Distance:
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DeviationDistanceNormalized2005 |
Normalized Deviation Distance:
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EditDistance |
Edit Distance:
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EditDistance |
EditDistance is an implementation of Wagner and Fischer's dynamic programming algorithm for computing string edit distance.
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ExactMatchDistance |
Exact Match Distance:
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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.
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InterchangeDistance |
Interchange Distance:
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JacobiDiagonalization |
This class uses Jacobi iteration to compute the eigenvalues and eigenvectors of a symmetric matrix, provided as a 2-D Java array.
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KendallTauDistance |
Kendall Tau Distance:
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KendallTauSequenceDistance |
Kendall Tau Sequence Distance is
the minimum number of adjacent swaps necessary to transform one sequence into the other.
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LeeDistance |
Lee Distance:
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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.
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MathFunctions |
MathFunctions is a class of utility methods that implement various mathematical functions.
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MatrixOps |
Utility class of basic linear algebra matrix operations, where matrices are
represented as 2-D Java arrays.
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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].
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Permutation |
Representation of a permutation of the integers from 0 to N-1, inclusive.
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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.
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PermutationDistanceMeasurer |
Implement this interface, PermutationDistanceMeasurer, to define a distance metric for permutations.
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PermutationDistanceMeasurerDouble |
Implement this interface, PermutationDistanceMeasurerDouble, to define a distance metric for permutations,
where the distance is a floating-point value.
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PermutationIterator |
Iterator over all permutations of a specified length, n, of the integers in the interval [0,n).
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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.
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ReinsertionDistance |
Reinsertion Distance:
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ReversalDistance |
Reversal Distance:
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ReversalIndependentDistance |
This class implements the concept of a reversal independent distance measure.
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ReversalIndependentDistanceDouble |
This class implements the concept of a reversal independent distance measure.
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RTypeDistance |
RType Distance:
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ScrambleDistance |
Scramble Distance:
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SequenceDistanceMeasurer |
Implement this interface, SequenceDistanceMeasurer, to define a distance metric for sequences.
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SequenceDistanceMeasurerDouble |
Implement this interface, SequenceDistanceMeasurerDouble, to define a distance metric for sequences.
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SequenceSampler |
ArraySampler is a class of utility methods related to
efficiently generating random samples of array elements, without replacement.
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SquaredDeviationDistance |
Squared Deviation Distance:
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Statistics |
Utility class of basic statistics.
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