See: Description
Interface | Description |
---|---|
AlignmentAlgorithm<X,Y,R> |
This is the most generic AlignmentAlgorithm interface for all algorithms that provide some sort
of alignment between two input sequences.
|
DerivableAlignmentDistance<X,Y> |
This is an interface to provide calculation methods for the gradient of an
alignment w.r.t.
|
Class | Description |
---|---|
AbstractStrictAlignmentAlgorithm<X,Y,R> |
This is an abstract super class implementing the Needleman-Wunsch-Algorithm or
Wagner-Fischer-Algorithm to compute a standard edit distance, also called Levenshtein-distance,
on input sequences.
|
AbstractStrictDTWAlgorithm<X,Y,R> |
This is an abstract super class implementing the dynamic time warping (DTW) dissimilarity.
|
Alignment<X,Y> |
This class models an Alignment as it is given out by a strict alignment.
|
AlignmentList<X,Y> |
This is a list-based datastructure accumulating multiple AlignmentPaths.
|
AlignmentMap<X,Y> |
This is a Map-based datastructure implementing a mapping from scores to Alignments.
|
ComparatorValidator |
This class has the sole purpose to validate that a Comparator supports all OperationTypes an
AlignmentAlgorithm requires.
|
CooptimalModel<X,Y> |
This is a sparse model of all co-optimal paths in an alignment matrix.
|
Operation<X,Y> |
This defines an applied Alignment Operation.
|
ParallelGradientEngine<X,Y> |
This allows parallel processing of gradient calculations.
|
ParallelProcessingEngine<X,Y,R> |
This allows parallel processing of alignment calculations.
|
Softmin |
This implements utility functions for the softmin function.
|
SquareParallelProcessingEngine<X,R> |
This allows parallel processing of alignment calculations.
|
StrictAlignmentAllOptimalAlgorithm<X,Y> |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
|
StrictAlignmentFullAlgorithm<X,Y> |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
|
StrictAlignmentScoreAlgorithm<X,Y> |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
|
StrictDTWFullAlgorithm<X,Y> |
This is an implementation of the AbstractStrictDTWAlgorithm to calculate just one exemplary
optimal DTW Alignment.
|
StrictDTWScoreAlgorithm<X,Y> |
This is an implementation of the AbstractStrictDTWAlgorithm to calculate just the normalized
score.
|
Enum | Description |
---|---|
DissimilarityWeighting |
This is a helper class to enable users to weight a collection of dissimilarities based on
different schemes specified below.
|
Copyright (C) 2016-2018 Benjamin Paaßen, AG Theoretical Computer Science, Centre of Excellence Cognitive Interaction Technology (CITEC), University of Bielefeld, licensed under the AGPL v. 3: http://openresearch.cit-ec.de/projects/tcs . This documentation is licensed under the conditions of CC-BY-SA 4.0: https://creativecommons.org/licenses/by-sa/4.0/