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 |
---|---|
static IllegalArgumentException |
ComparatorValidator.checkValidity(Grammar grammar,
Comparator comp)
Checks whether the given Comparator supports all OperationType the given Grammar
requires and returns an IllegalArgumentException if it does not.
|
static boolean |
ComparatorValidator.isValid(Grammar grammar,
Comparator comp)
Returns true if and only if the given Comparator supports all OperationType the given
Grammar requires.
|
static void |
ComparatorValidator.validate(Grammar grammar,
Comparator comp)
Checks whether the given Comparator supports all OperationType the given Grammar
requires and throws an IllegalArgumentException if it does not.
|
Constructor and Description |
---|
AbstractADPAlgorithm(Grammar<N> grammar,
Class<R> resultClass,
Comparator<X,Y> comparator) |
SoftADPFullAlgorithm(Grammar<N> grammar,
Comparator<X,Y> comparator)
Creates a new SoftFullAlgorithm based on the given ADP grammar
and the given Comparator/algebra.
|
SoftADPPathModel(Comparator<X,Y> comparator,
Grammar<N> grammar,
double beta,
double approxThreshold,
double distance,
EnumMap<N,double[][]> dpTables,
EnumMap<OperationType,double[][]> repMatrices,
EnumMap<OperationType,double[]> delVectors,
EnumMap<OperationType,double[]> insVectors,
List<X> left,
List<Y> right) |
SoftADPScoreAlgorithm(Grammar<N> grammar,
Comparator<X,Y> comparator) |
StrictADPCooptimalAlgorithm(Grammar<N> grammar,
Comparator<X,Y> comparator) |
StrictADPFullAlgorithm(Grammar<N> grammar,
Comparator<X,Y> comparator) |
StrictADPScoreAlgorithm(Grammar<N> grammar,
Comparator<X,Y> comparator) |
Copyright (C) 2016 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/