See: Description
Interface | Description |
---|---|
Grammar<N extends Enum<N>> |
An Algebraic Dynamic Programming (ADP) grammar is a regular tree
grammar.
|
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.
|
Class | Description |
---|---|
AbstractADPAlgorithm<X,Y,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.
|
AffineGrammar |
This grammar describes affine (and local) sequence alignment as
described by Smith and Waterman (1981) and Gotoh (1982).
|
ComparatorValidator |
This class has the sole purpose to validate that a Comparator supports all OperationTypes a
Grammar requires.
|
DPCellId |
This identifies a cell in the dynamic programming tables by the ordinal of
the nonterminal symbol, the index in the left sequence (i) and the index
in the right sequence (j).
|
DTWGrammar |
This is a grammar for dynamic time warping.
|
FlexibleGrammar<N extends Enum<N>> |
This is a flexible grammar implementation that allows users to
create new grammars at runtime.
|
FlexibleGrammar.RuleAvailabilityMatrix<N extends Enum<N>> | |
GlobalAsymmetricGrammar |
This is a slight variation of the global alignment grammar.
|
GlobalGrammar |
This is the most basic (and classic) alignment grammar there is.
|
ProductionRule<N extends Enum<N>> |
A ProductionRule actually represents the right hand side of a
production rule in an ADP grammar.
|
SakoeChibaDTWGrammar |
This is a grammar for dynamic time warping.
|
SoftADPFullAlgorithm<X,Y,N extends Enum<N>> |
This algorithm returns a SoftADPPathModel based on the given grammar
and algebra/Comparator.
|
SoftADPPathModel<X,Y,N extends Enum<N>> |
This is basically a large storage class for all results of a
SoftADPFullAlgorithm to facilitate derivative calculation.
|
SoftADPScoreAlgorithm<X,Y,N extends Enum<N>> |
This algorithm calculates the soft alignment score for the given
input grammar and algebra/Comparator.
|
SparseAbstractADPAlgorithm<X,Y,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 sparse grammar.
|
SparseAbstractADPAlgorithm.SparseMatrix |
This is the SparseMatrix class we use within this algorithm.
|
SparseStrictADPFullAlgorithm<X,Y,N extends Enum<N>> |
This algorithm calculates an optimal AlignmentPath using the given ADP grammar and
algebra/Comparator.
|
SparseStrictADPScoreAlgorithm<X,Y,N extends Enum<N>> |
This algorithm calculates the strict alignment score for the given input grammar and
algebra/Comparator.
|
StrictADPCooptimalAlgorithm<X,Y,N extends Enum<N>> |
This algorithm calculates all co-optimal paths in form of a CooptimalModel
|
StrictADPFullAlgorithm<X,Y,N extends Enum<N>> |
This algorithm calculates an optimal AlignmentPath using the given ADP grammar and
algebra/Comparator.
|
StrictADPScoreAlgorithm<X,Y,N extends Enum<N>> |
This algorithm calculates the strict alignment score for the given input grammar and
algebra/Comparator.
|
Enum | Description |
---|---|
AffineGrammar.Nonterminal |
These are the nonterminal symbols for the affine grammar.
|
DTWGrammar.Nonterminal | |
GlobalAsymmetricGrammar.Nonterminal | |
GlobalGrammar.Nonterminal | |
SakoeChibaDTWGrammar.Nonterminal |
Exception | Description |
---|---|
GrammarValidityException |
This exception is thrown if a flexible grammar is invalid.
|
Copyright (C) 2016-2018 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/