See: Description
Interface | Description |
---|---|
AlignmentAlgorithm<R> |
This is the most generic AlignmentAlgorithm interface for all algorithms
that provide some sort of alignment between two input sequences.
|
AlignmentDerivativeAlgorithm |
This is an interface to provide calculation methods for the derivative of an
alignment w.r.t. a specific comparator and the weights for the keywords.
|
AlignmentMatrixEntry |
This is an interface for the entries of an alignment matrix.
|
GapAlignmentAlgorithm<R> |
This is an interface for Alignment algorithms that use gaps (insertion and
deletion operations) in the alignment.
|
LocalAlignmentAlgorithm<R> |
This is an interface for GapAlignmentAlgorithms that also use skips
(SkipDeletion, SkipInsertion) and in that way are local distance measures.
|
Class | Description |
---|---|
AbstractGapAlignmentAlgorithm<X extends AlignmentMatrixEntry,R> |
This is an abstract super class for GapAlignmentAlgorithms that provides a
generic implementation of the dynamic programming needed to efficiently
calculate the alignment.
|
AbstractLocalAlignmentAlgorithm<R> |
This is an implementation of the local alignment algorithm scheme
combining actually two approaches: First the algorithm of Gotoh et al.
|
AbstractStrictDTWAlgorithm<R> |
This serves as an abstract super class for strict Dynamic Time Warping
implementations.
|
AlignmentPath |
This class models an alignment path as it is given out by a strict alignment.
|
AlignmentSpecification |
The alignment specification defines which keywords of the input sequences
shall be used and which comparator is to be used to calculate the local
distance between two values for that keyword.
|
Counter |
Just a very simple counting class.
|
DynamicTimeWarpingAlgorithm |
Implements soft alignment DTW.
|
IndexedStochasticPriorityQueue<K extends Comparable<K>,V> |
This is a helper class, which actually extends the TreeMap to implement a
PriorityQueue that is able to poll the minimum as well as the maximum in
constanst time.
|
MatrixCoordinate |
Identifies a position in a two-dimensional matrix.
|
Operation |
This defines an applied alignment operation.
|
ParallelDerivativeEngine |
This allows parallel processing of derivative calculations.
|
ParallelProcessingEngine<R> |
This allows parallel processing of alignment calculations.
|
PathList |
This is a list-based datastructure accumulating multiple AlignmentPaths.
|
PathMap |
This is a TreeMap-based datastructure implementing a mapping from scores to
AlignmentPaths.
|
SoftAlignmentFullAlgorithm |
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
|
SoftAlignmentSamplingAlgorithm |
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
|
SoftAlignmentScoreAlgorithm |
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
|
SoftAlignmentScoreAlgorithm.ScoreEntry | |
SoftDTWModel |
storage unit for soft DTW alignment result, provides functions to calculate
the soft DTW derivatives based on the stored soft alignment
|
SoftLocalAlignmentFullAlgorithm |
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
SoftLocalAlignmentScoreAlgorithm |
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
SoftLocalPathModel |
This is basically a storage for the DTW matrix of the
SoftLocalAlignmentAlgorithm.
|
Softmin |
This implements utility functions for the softmin function.
|
SoftPathModel |
This is the soft pendant to the AlignmentPath.
|
SoftPathModel.SoftMatrixEntry | |
SparseMatrix<X> |
This models a sparse matrix that does not have to be fully calculated.
|
StrictAlignmentFullAlgorithm |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
StrictAlignmentFullAlgorithm.FullMatrixEntry | |
StrictAlignmentScoreAlgorithm |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
StrictAlignmentScoreAlgorithm.ScoreEntry | |
StrictAllOptimalAlgorithm |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
StrictAllOptimalAlgorithm.FullMatrixEntry | |
StrictDTWFullAlgorithm |
This is an implementation of the AbstractStrictDTWAlgorithm to
calculate just one exemplary optimal DTW path.
|
StrictDTWScoreAlgorithm |
This is an implementation of the AbstractStrictDTWAlgorithm to
calculate just the score.
|
StrictKPathAlgorithm |
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
StrictLocalAlignmentFullAlgorithm |
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
StrictLocalAlignmentScoreAlgorithm |
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
Enum | Description |
---|---|
AbstractLocalAlignmentAlgorithm.Recurrence | |
OperationType |
This defines the possible types of operations that may be used in an
alignment within this Toolbox.
|
ScoreBasedWeighting |
This is a helper class to enable users to weight a collection of scores based
on different schemes specified below.
|
Copyright (C) 2013, 2014 Benjamin Paaßen, Charlie Krüger, Georg Zentgraf, 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