Package | Description |
---|---|
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.
|
Modifier and Type | Interface and Description |
---|---|
interface |
SparseGrammar<N extends Enum<N>>
This is a special kind of ADP grammar, that limits the dynamic programming
matrix to a few cells and thus supports a sparse dynamic programming matrix,
which (ideally) reduces the runtime to linear time.
|
Modifier and Type | Class and Description |
---|---|
class |
AffineGrammar
This grammar describes affine (and local) sequence alignment as
described by Smith&Waterman (1981) and Gotoh (1982).
|
class |
DTWGrammar
This is a grammar for dynamic time warping.
|
class |
FlexibleGrammar<N extends Enum<N>>
This is a flexible grammar implementation that allows users to
create new grammars at runtime.
|
class |
GlobalAsymmetricGrammar
This is a slight variation of the global alignment grammar.
|
class |
GlobalGrammar
This is the most basic (and classic) alignment grammar there is.
|
class |
SakoeChibaDTWGrammar
This is a grammar for dynamic time warping.
|
Modifier and Type | Method and Description |
---|---|
Grammar<N> |
AbstractADPAlgorithm.getGrammar()
Returns the ADP grammar that is used as basis of this ADPAlgorithm.
|
Grammar<N> |
SoftADPPathModel.getGrammar()
Returns the ADP grammar that was used to compute this SoftADPPathModel.
|
Modifier and Type | Method and Description |
---|---|
static <N extends Enum<N>> |
SoftADPPathModel.getGenericClass(Grammar<N> grammar)
Returns the generic class of a SoftADPPathModel given a grammar.
|
Constructor and Description |
---|
AbstractADPAlgorithm(Grammar<N> grammar,
Class<R> resultClass,
AlignmentSpecification alignmentSpecification) |
SoftADPFullAlgorithm(Grammar<N> grammar,
AlignmentSpecification alignmentSpecification)
Creates a new SoftFullAlgorithm based on the given ADP grammar
and the given AlignmentSpecification/algebra.
|
SoftADPPathModel(AlignmentSpecification specification,
Grammar<N> grammar,
double beta,
double approxThreshold,
double distance,
EnumMap<N,double[][]> dpTables,
double[][] compareMatrix,
double[] deletionMatrix,
double[] insertionMatrix,
double[] skipDeletionMatrix,
double[] skipInsertionMatrix,
Sequence leftSequence,
Sequence rightSequence) |
SoftADPScoreAlgorithm(Grammar<N> grammar,
AlignmentSpecification alignmentSpecification) |
StrictADPFullAlgorithm(Grammar<N> grammar,
AlignmentSpecification alignmentSpecification) |
StrictADPScoreAlgorithm(Grammar<N> grammar,
AlignmentSpecification alignmentSpecification) |
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/