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.forests |
This package contains tree edit distance algorithms for forests.
|
de.citec.tcs.alignment.learning |
This module is a custom implementation of the Large Margin
Nearest Neighbor classification scheme of Weinberger, Saul, et al. (2009).
|
de.citec.tcs.alignment.sets |
This module provides algorithms to compare sets, that is, order-invariant lists.
|
de.citec.tcs.alignment.wrappers |
This module contains some wrappers to make usage of the
TCSAlignmentToolbox easier.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractStrictAlignmentAlgorithm<X,Y,R>
This is an abstract super class implementing the Needleman-Wunsch-Algorithm or
Wagner-Fischer-Algorithm to compute a standard edit distance, also called Levenshtein-distance,
on input sequences.
|
class |
AbstractStrictDTWAlgorithm<X,Y,R>
This is an abstract super class implementing the dynamic time warping (DTW) dissimilarity.
|
class |
StrictAlignmentAllOptimalAlgorithm<X,Y>
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
|
class |
StrictAlignmentFullAlgorithm<X,Y>
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
|
class |
StrictAlignmentScoreAlgorithm<X,Y>
This is an implementation of the Needleman-Wunsch-Algorithm for sequence alignment.
|
class |
StrictDTWFullAlgorithm<X,Y>
This is an implementation of the AbstractStrictDTWAlgorithm to calculate just one exemplary
optimal DTW Alignment.
|
class |
StrictDTWScoreAlgorithm<X,Y>
This is an implementation of the AbstractStrictDTWAlgorithm to calculate just the normalized
score.
|
Modifier and Type | Method and Description |
---|---|
static <X,Y> IllegalArgumentException |
ComparatorValidator.checkValidity(AlignmentAlgorithm<X,Y,?> algorithm,
Comparator<? extends X,? extends Y> comp)
Checks whether the given Comparator supports all OperationType the given AlignmentAlgorithm
requires and returns an IllegalArgumentException if it does not.
|
static <X,Y> boolean |
ComparatorValidator.isValid(AlignmentAlgorithm<X,Y,?> algorithm,
Comparator<? extends X,? extends Y> comp)
Returns true if and only if the given Comparator supports all OperationType the given
AlignmentAlgorithm requires.
|
static <X,Y> void |
ComparatorValidator.validate(AlignmentAlgorithm<X,Y,?> algorithm,
Comparator<? extends X,? extends Y> comp)
Checks whether the given Comparator supports all OperationType the given AlignmentAlgorithm
requires and throws an IllegalArgumentException if it does not.
|
Constructor and Description |
---|
ParallelProcessingEngine(AlignmentAlgorithm<X,Y,R> algorithm,
List<? extends List<X>> leftSequences,
List<? extends List<Y>> rightSequences)
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm
and the given Sequences.
|
SquareParallelProcessingEngine(AlignmentAlgorithm<X,X,R> algorithm,
List<? extends List<X>> sequences)
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm
and the given Sequences.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractADPAlgorithm<X,Y,R,N extends Enum<N>>
This is the most abstract ADP algorithm just implementing the
forward calculation of the dynamic programming tables for an
arbitrary grammar.
|
class |
SoftADPFullAlgorithm<X,Y,N extends Enum<N>>
This algorithm returns a SoftADPPathModel based on the given grammar
and algebra/Comparator.
|
class |
SoftADPScoreAlgorithm<X,Y,N extends Enum<N>>
This algorithm calculates the soft alignment score for the given
input grammar and algebra/Comparator.
|
class |
SparseAbstractADPAlgorithm<X,Y,R,N extends Enum<N>>
This is the most abstract ADP algorithm just implementing the forward calculation of the dynamic
programming tables for an arbitrary sparse grammar.
|
class |
SparseStrictADPFullAlgorithm<X,Y,N extends Enum<N>>
This algorithm calculates an optimal AlignmentPath using the given ADP grammar and
algebra/Comparator.
|
class |
SparseStrictADPScoreAlgorithm<X,Y,N extends Enum<N>>
This algorithm calculates the strict alignment score for the given input grammar and
algebra/Comparator.
|
class |
StrictADPCooptimalAlgorithm<X,Y,N extends Enum<N>>
This algorithm calculates all co-optimal paths in form of a CooptimalModel
|
class |
StrictADPFullAlgorithm<X,Y,N extends Enum<N>>
This algorithm calculates an optimal AlignmentPath using the given ADP grammar and
algebra/Comparator.
|
class |
StrictADPScoreAlgorithm<X,Y,N extends Enum<N>>
This algorithm calculates the strict alignment score for the given input grammar and
algebra/Comparator.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractForestAlgorithm<X,Y,R>
This AlignmentAlgorithm implements an edit distance on forests based on the Zhang & Shasha
algorithm (1989) for the tree edit distance.
|
class |
OrderedForestCooptimalAlgorithm<X,Y>
This AlignmentAlgorithm implements an edit distance on forests based on the Zhang & Shasha
algorithm (1989) for the tree edit distance.
|
class |
OrderedForestFullAlgorithm<X,Y>
This AlignmentAlgorithm implements an edit distance on forests based on the Zhang & Shasha
tree edit distance algorithm (1989).
|
class |
OrderedForestScoreAlgorithm<X,Y>
This AlignmentAlgorithm implements an edit distance on forests based on the Zhang & Shasha
algorithm (1989) for the tree edit distance.
|
class |
OrderedForestSoftAlgorithm<X,Y>
This AlignmentAlgorithm implements an edit distance on forests based on the Zhang & Shasha
algorithm (1989) for the tree edit distance.
|
class |
UnorderedForestCooptimalAlgorithm<X,Y>
This AlignmentAlgorithm implements an edit distance on forests based on the Zhang & Shasha
algorithm (1989) for the tree edit distance.
|
class |
UnorderedForestFullAlgorithm<X,Y>
This AlignmentAlgorithm implements an edit distance on forests based on the Zhang & Shasha
algorithm (1989) for the tree edit distance.
|
class |
UnorderedForestScoreAlgorithm<X,Y>
This AlignmentAlgorithm implements an edit distance on forests based on the Zhang & Shasha
algorithm (1989) for the tree edit distance.
|
class |
UnorderedForestSoftAlgorithm<X,Y>
This AlignmentAlgorithm implements an edit distance on forests based on the Zhang & Shasha
algorithm (1989) for the tree edit distance.
|
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 |
AbstractGreedySetAlignmentAlgorithm<X,Y,R>
This is an abstract super class providing a greedy solution approach to the optimal set alignment
problem.
|
class |
AbstractStrictSetAlignmentAlgorithm<X,Y,R>
This is an abstract super class solving the optimal set alignment problem via the Hungarian
algorithm for the assignment problem.
|
class |
GreedySetAlignmentFullAlgorithm<X,Y>
This is an implementation of the Hungarian algorithm for the optimal set alignment.
|
class |
GreedySetAlignmentScoreAlgorithm<X,Y>
This is an implementation of the greedy algorithm for the optimal set alignment.
|
class |
StrictSetAlignmentFullAlgorithm<X,Y>
This is an implementation of the Hungarian algorithm for the optimal set alignment.
|
class |
StrictSetAlignmentScoreAlgorithm<X,Y>
This is an implementation of the Hungarian algorithm for the optimal set alignment.
|
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.
|
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.
|
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/