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 | Interface and Description |
---|---|
interface |
GapAlignmentAlgorithm<R>
This is an interface for Alignment algorithms that use gaps (insertion and
deletion operations) in the alignment.
|
interface |
SkipAlignmentAlgorithm<R>
This is an interface for GapAlignmentAlgorithms that also use skips
(SkipDeletion, SkipInsertion) and in that way are local distance measures.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractAffineAlignmentAlgorithm<R>
This is an implementation of the affine alignment algorithm scheme
combining actually two approaches: First the algorithm of Gotoh et al.
|
class |
AbstractGapAlignmentAlgorithm<X extends AlignmentMatrixEntry,R>
This is an abstract super class for GapAlignmentAlgorithms that provides a
generic implementation of the dynamic programming needed to efficiently
calculate the alignment.
|
class |
AbstractStrictDTWAlgorithm<R>
This serves as an abstract super class for strict Dynamic Time Warping
implementations.
|
class |
KernelDTWFullAlgorithm
Implements soft alignment DTW.
|
class |
SoftAffineAlignmentFullAlgorithm
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
class |
SoftAffineAlignmentScoreAlgorithm
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
class |
SoftAlignmentFullAlgorithm
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
|
class |
SoftAlignmentSamplingAlgorithm
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
|
class |
SoftAlignmentScoreAlgorithm
This calculates the soft (global) alignment of two sequences similarly to the
Needleman-Wunsch-Algorithm.
|
class |
StrictAffineAlignmentFullAlgorithm
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
class |
StrictAffineAlignmentScoreAlgorithm
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
class |
StrictAlignmentFullAlgorithm
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
class |
StrictAlignmentScoreAlgorithm
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
class |
StrictAllOptimalAlgorithm
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
class |
StrictDTWFullAlgorithm
This is an implementation of the AbstractStrictDTWAlgorithm to
calculate just one exemplary optimal DTW path.
|
class |
StrictDTWScoreAlgorithm
This is an implementation of the AbstractStrictDTWAlgorithm to
calculate just the score.
|
class |
StrictKPathAlgorithm
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
Modifier and Type | Method and Description |
---|---|
AlignmentAlgorithm<R> |
ParallelProcessingEngine.getAlgorithm() |
Constructor and Description |
---|
ParallelProcessingEngine(AlignmentAlgorithm<R> algorithm,
Sequence[] sequences)
This sets up a ParallelProcessingEngine for the given AlignmentAlgorithm
and the given Sequences.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractADPAlgorithm<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<N extends Enum<N>>
This algorithm returns a SoftADPPathModel based on the given grammar
and algebra/AlignmentSpecification.
|
class |
SoftADPScoreAlgorithm<N extends Enum<N>>
This algorithm calculates the soft alignment score for the given
input grammar and algebra/AlignmentSpecification.
|
class |
StrictADPFullAlgorithm<N extends Enum<N>>
This algorithm calculates an optimal AlignmentPath using the given
ADP grammar and algebra/AlignmentSpecification.
|
class |
StrictADPScoreAlgorithm<N extends Enum<N>>
This algorithm calculates the strict alignment score for the given
input grammar and algebra/AlignmentSpecification.
|
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.
|
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.
|
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