Package | Description |
---|---|
de.citec.tcs.alignment |
This module defines the interface for AlignmentAlgorithms as
well as some helper classes.
|
de.citec.tcs.alignment.adp |
This package contains a more general approach to construct
AlignmentAlgorithms by relying on the theoretical concept of Algebraic
Dynamic Programming (ADP) as developed by Giegerich et al.
|
de.citec.tcs.alignment.learning |
This module is a custom implementation of the Large Margin
Nearest Neighbor classification scheme of Weinberger, Saul, et al.
|
de.citec.tcs.alignment.visualization |
This module contains means to visualize AlignmentPaths.
|
de.citec.tcs.alignment.wrappers |
This module contains some wrappers to make usage of the
TCSAlignmentToolbox easier.
|
Class and Description |
---|
AbstractAffineAlignmentAlgorithm
This is an implementation of the affine alignment algorithm scheme
combining actually two approaches: First the algorithm of Gotoh et al.
|
AbstractAffineAlignmentAlgorithm.Recurrence |
AbstractGapAlignmentAlgorithm
This is an abstract super class for GapAlignmentAlgorithms that provides a
generic implementation of the dynamic programming needed to efficiently
calculate the alignment.
|
AbstractParallelDerivativeEngine |
AbstractStrictDTWAlgorithm
This serves as an abstract super class for strict Dynamic Time Warping
implementations.
|
AlignmentAlgorithm
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.
|
AlignmentMatrixEntry
This is an interface for the entries of an alignment matrix.
|
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.
|
GapAlignmentAlgorithm
This is an interface for Alignment algorithms that use gaps (insertion and
deletion operations) in the alignment.
|
Operation
This defines an applied alignment operation.
|
PathList
This is a list-based datastructure accumulating multiple AlignmentPaths.
|
PathMap
This is a TreeMap-based datastructure implementing a mapping from scores to
AlignmentPaths.
|
ScoreBasedWeighting
This is a helper class to enable users to weight a collection of scores based
on different schemes specified below.
|
SkipAlignmentAlgorithm
This is an interface for GapAlignmentAlgorithms that also use skips
(SkipDeletion, SkipInsertion) and in that way are local distance measures.
|
SoftAffinePathModel
This is basically a storage for the DP matrix of the
SoftAffineAlignmentAlgorithm.
|
SoftAlignmentScoreAlgorithm.ScoreEntry |
SoftDTWModel
storage unit for soft DTW alignment result, provides functions to calculate
the soft DTW derivatives based on the stored soft alignment
|
SoftPathModel
This is the soft pendant to the AlignmentPath.
|
SoftPathModel.SoftMatrixEntry |
StrictAlignmentFullAlgorithm.FullMatrixEntry |
StrictAlignmentScoreAlgorithm.ScoreEntry |
StrictAllOptimalAlgorithm.FullMatrixEntry |
Class and Description |
---|
AlignmentAlgorithm
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.
|
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.
|
Class and Description |
---|
AlignmentAlgorithm
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.
|
Class and Description |
---|
AlignmentPath
This class models an alignment path as it is given out by a strict alignment.
|
Operation
This defines an applied alignment operation.
|
Class and Description |
---|
AlignmentAlgorithm
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.
|
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.
|
Copyright (C) 2013-2015 Benjamin Paaßen, 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 . This documentation is licensed under the conditions of CC-BY-SA 4.0: https://creativecommons.org/licenses/by-sa/4.0/