Package | Description |
---|---|
de.unibi.citec.tcs.alignment |
This package contains the actual AlignmentAlgorithms as well as their return
classes.
|
de.unibi.citec.tcs.alignment.wrappers |
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 |
LocalAlignmentAlgorithm<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 |
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 |
AbstractLocalAlignmentAlgorithm<R>
This is an implementation of the local alignment algorithm scheme
combining actually two approaches: First the algorithm of Gotoh et al.
|
class |
AbstractStrictDTWAlgorithm<R>
This serves as an abstract super class for strict Dynamic Time Warping
implementations.
|
class |
DynamicTimeWarpingAlgorithm
Implements soft alignment DTW.
|
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 |
SoftLocalAlignmentFullAlgorithm
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
class |
SoftLocalAlignmentScoreAlgorithm
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.
|
class |
StrictLocalAlignmentFullAlgorithm
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
class |
StrictLocalAlignmentScoreAlgorithm
This implements a local affine alignment similar to Smith-Waterman
and Gotoh.
|
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 | 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, 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