Package | Description |
---|---|
de.citec.tcs.alignment |
This module defines the interface for AlignmentAlgorithms as
well as some helper classes.
|
Modifier and Type | Interface and Description |
---|---|
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 |
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 |
StrictKPathAlgorithm
This is an implementation of the Needleman-Wunsch-Algorithm for sequence
alignment.
|
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 . This documentation is licensed under the conditions of CC-BY-SA 4.0: https://creativecommons.org/licenses/by-sa/4.0/