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.trees |
This package contains an implementation of the Tree Edit Distance according to Zhang & Shasha (1989).
|
de.citec.tcs.alignment.wrappers |
This module contains some wrappers to make usage of the
TCSAlignmentToolbox easier.
|
Modifier and Type | Class and Description |
---|---|
class |
Alignment<X,Y>
This class models an Alignment as it is given out by a strict alignment.
|
class |
AlignmentList<X,Y>
This is a list-based datastructure accumulating multiple AlignmentPaths.
|
class |
AlignmentMap<X,Y>
This is a Map-based datastructure implementing a mapping from scores to Alignments.
|
class |
CooptimalModel<X,Y>
This is a sparse model of all co-optimal paths in an alignment matrix.
|
Modifier and Type | Method and Description |
---|---|
Map<MatrixEngine.MatrixCoordinate,DerivableAlignmentDistance<X,Y>> |
ParallelGradientEngine.getDistances()
Returns the DerivableAlignmentDistance objects used for derivative calculation.
|
Constructor and Description |
---|
ParallelGradientEngine(DerivableAlignmentDistance<X,Y>[][] derivableMatrixEntries,
DerivableComparator<X,Y> comparator)
Creates a ParallelGradientEngine that computes gradients for several
DeriableAlignmentDistance objects in parallel.
|
Constructor and Description |
---|
ParallelGradientEngine(Collection<Engine.CalculationResult<? extends MatrixEngine.MatrixCoordinate,? extends DerivableAlignmentDistance<X,Y>>> results,
int M,
int N,
DerivableComparator<X,Y> comparator)
Creates a ParallelGradientEngine that computes gradients for several
DeriableAlignmentDistance objects in parallel.
|
ParallelGradientEngine(Map<MatrixEngine.MatrixCoordinate,DerivableAlignmentDistance<X,Y>> derivableMatrixEntries,
int M,
int N,
DerivableComparator<X,Y> comparator)
Creates a ParallelGradientEngine that computes gradients for several
DeriableAlignmentDistance objects in parallel.
|
Modifier and Type | Class and Description |
---|---|
class |
SoftADPPathModel<X,Y,N extends Enum<N>>
This is basically a large storage class for all results of a
SoftADPFullAlgorithm to facilitate derivative calculation.
|
Constructor and Description |
---|
LMNNGradientCalculator(List<? extends List<X>> data,
int[] trainingLabels,
AlignmentAlgorithm<X,X,? extends DerivableAlignmentDistance<X,X>> algo) |
Modifier and Type | Class and Description |
---|---|
class |
CooptimalMatrix<X,Y>
This object stores a matrix indicating the pairings of nodes in both inputs with can be part
of a co-optimal alignment.
|
Modifier and Type | Method and Description |
---|---|
static <R extends DerivableAlignmentDistance<Node,Node>> |
StringEditDistance.calculateDerivatives(AlignmentAlgorithm<Node,Node,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<Node,Node,? extends DerivableAlignmentDistance<Node,Node>> algorithm,
Sequence a,
Sequence b)
Calculates the alignment derivative between the two given input sequences
using the given algorithm.
|
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/