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.wrappers |
This module contains some wrappers to make usage of the
TCSAlignmentToolbox easier.
|
Modifier and Type | Class and Description |
---|---|
class |
AlignmentPath
This class models an alignment path as it is given out by a strict alignment.
|
class |
PathList
This is a list-based datastructure accumulating multiple AlignmentPaths.
|
class |
PathMap
This is a TreeMap-based datastructure implementing a mapping from scores to
AlignmentPaths.
|
class |
SoftAffinePathModel
This is basically a storage for the DP matrix of the
SoftAffineAlignmentAlgorithm.
|
class |
SoftDTWModel
storage unit for soft DTW alignment result, provides functions to calculate
the soft DTW derivatives based on the stored soft alignment
|
class |
SoftPathModel
This is the soft pendant to the AlignmentPath.
|
Modifier and Type | Method and Description |
---|---|
Callable<double[]> |
ParallelRawDerivativeEngine.createCallableWithAlgorithm(AlignmentDerivativeAlgorithm algo)
Instead of a matrix coordinate identifier, this method should create a
fitting calculation job for the derivative with the given
AlignmentDerivativeAlgorithm.
|
Callable<Y> |
ParallelDerivativeEngine.createCallableWithAlgorithm(AlignmentDerivativeAlgorithm algo)
Instead of a matrix coordinate identifier, this method should create a
fitting calculation job for the derivative with the given
AlignmentDerivativeAlgorithm.
|
abstract Callable<R> |
AbstractParallelDerivativeEngine.createCallableWithAlgorithm(AlignmentDerivativeAlgorithm algo)
Instead of a matrix coordinate identifier, this method should create a
fitting calculation job for the derivative with the given
AlignmentDerivativeAlgorithm.
|
Callable<double[]> |
ParallelWeightDerivativeEngine.createCallableWithAlgorithm(AlignmentDerivativeAlgorithm algo)
Instead of a matrix coordinate identifier, this method should create a
fitting calculation job for the derivative with the given
AlignmentDerivativeAlgorithm.
|
Constructor and Description |
---|
AbstractParallelDerivativeEngine(AlignmentDerivativeAlgorithm[][] derivableMatrixEntries,
Class<R> resultClass) |
ParallelDerivativeEngine(AlignmentDerivativeAlgorithm[][] derivableMatrixEntries,
DerivableComparator<?,Y> comparator,
String keyword) |
ParallelRawDerivativeEngine(AlignmentDerivativeAlgorithm[][] derivableMatrixEntries,
DerivableComparator<?,?> comparator,
String keyword) |
ParallelWeightDerivativeEngine(AlignmentDerivativeAlgorithm[][] derivableMatrixEntries) |
Constructor and Description |
---|
AbstractParallelDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N,
Class<R> resultClass) |
ParallelDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N,
DerivableComparator<?,Y> comparator,
String keyword) |
ParallelRawDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N,
DerivableComparator<?,?> comparator,
String keyword) |
ParallelWeightDerivativeEngine(Map<MatrixEngine.MatrixCoordinate,AlignmentDerivativeAlgorithm> derivableMatrixEntries,
int M,
int N) |
Modifier and Type | Class and Description |
---|---|
class |
SoftADPPathModel<N extends Enum<N>>
This is basically a large storage class for all results of a
SoftADPFullAlgorithm to facilitate derivative calculation.
|
Modifier and Type | Method and Description |
---|---|
static <R extends AlignmentDerivativeAlgorithm> |
StringEditDistance.calculateDerivatives(AlignmentAlgorithm<R> algorithm,
Sequence[] dataSpace,
int threadNum)
Calculates the pairwise alignment derivative between all given input
sequences using the given algorithm.
|
Modifier and Type | Method and Description |
---|---|
static double[][] |
StringEditDistance.calculateDerivative(AlignmentAlgorithm<? extends AlignmentDerivativeAlgorithm> algorithm,
Sequence a,
Sequence b)
Calculates the alignment derivative between the two given input sequences
using the given algorithm.
|
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