Package | Description |
---|---|
de.unibi.citec.tcs.alignment |
This package contains the actual AlignmentAlgorithms as well as their return
classes.
|
de.unibi.citec.tcs.alignment.comparators |
This package contains comparators that define distances between Values.
|
de.unibi.citec.tcs.alignment.visualization | |
de.unibi.citec.tcs.alignment.wrappers |
Class and Description |
---|
AbstractGapAlignmentAlgorithm
This is an abstract super class for GapAlignmentAlgorithms that provides a
generic implementation of the dynamic programming needed to efficiently
calculate the alignment.
|
AbstractLocalAlignmentAlgorithm
This is an implementation of the local alignment algorithm scheme
combining actually two approaches: First the algorithm of Gotoh et al.
|
AbstractLocalAlignmentAlgorithm.Recurrence |
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. a specific comparator and the weights for the keywords.
|
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.
|
LocalAlignmentAlgorithm
This is an interface for GapAlignmentAlgorithms that also use skips
(SkipDeletion, SkipInsertion) and in that way are local distance measures.
|
Operation
This defines an applied alignment operation.
|
OperationType
This defines the possible types of operations that may be used in an
alignment within this Toolbox.
|
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.
|
SoftAlignmentScoreAlgorithm.ScoreEntry |
SoftDTWModel
storage unit for soft DTW alignment result, provides functions to calculate
the soft DTW derivatives based on the stored soft alignment
|
SoftLocalPathModel
This is basically a storage for the DTW matrix of the
SoftLocalAlignmentAlgorithm.
|
SoftPathModel
This is the soft pendant to the AlignmentPath.
|
SoftPathModel.SoftMatrixEntry |
StrictAlignmentFullAlgorithm.FullMatrixEntry |
StrictAlignmentScoreAlgorithm.ScoreEntry |
StrictAllOptimalAlgorithm.FullMatrixEntry |
Class and Description |
---|
OperationType
This defines the possible types of operations that may be used in an
alignment within this Toolbox.
|
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. a specific comparator and the weights for the keywords.
|
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, 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